Fold 0
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': None,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': None,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_0',
 'save_smiles_splits': False,
 'seed': 0,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': None,
 'test': False,
 'test_fold_index': None,
 'train_data_size': None,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 0
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.747418
Best score so far is 0.747418 at epoch 0 
Epoch 1
Validation auc = 0.764319
Best score so far is 0.764319 at epoch 1 
Epoch 2
Validation auc = 0.780282
Best score so far is 0.780282 at epoch 2 
Epoch 3
Validation auc = 0.792958
Best score so far is 0.792958 at epoch 3 
Epoch 4
Loss = 1.3238e-02, PNorm = 43.6397, GNorm = 4.7442, lr_0 = 6.5000e-04
Validation auc = 0.799061
Best score so far is 0.799061 at epoch 4 
Epoch 5
Validation auc = 0.807042
Best score so far is 0.807042 at epoch 5 
Epoch 6
Validation auc = 0.805634
Epoch 7
Validation auc = 0.793427
Epoch 8
Validation auc = 0.799061
Epoch 9
Loss = 1.1747e-02, PNorm = 43.6973, GNorm = 2.7196, lr_0 = 9.9743e-04
Validation auc = 0.771831
Epoch 10
Validation auc = 0.753052
Epoch 11
Validation auc = 0.744131
Epoch 12
Validation auc = 0.740376
Epoch 13
Validation auc = 0.746948
Epoch 14
Loss = 7.9677e-03, PNorm = 43.7691, GNorm = 2.3326, lr_0 = 9.8890e-04
Validation auc = 0.738498
Epoch 15
Validation auc = 0.725352
Epoch 16
Validation auc = 0.715023
Epoch 17
Validation auc = 0.712207
Epoch 18
Validation auc = 0.710329
Epoch 19
Loss = 8.9759e-03, PNorm = 43.8308, GNorm = 2.2127, lr_0 = 9.8045e-04
Validation auc = 0.723005
Epoch 20
Validation auc = 0.749296
Epoch 21
Validation auc = 0.747418
Epoch 22
Validation auc = 0.744131
Epoch 23
Validation auc = 0.744601
Epoch 24
Loss = 8.0627e-03, PNorm = 43.8863, GNorm = 1.8582, lr_0 = 9.7207e-04
Validation auc = 0.737089
Epoch 25
Validation auc = 0.724413
Epoch 26
Validation auc = 0.719718
Epoch 27
Validation auc = 0.700939
Epoch 28
Validation auc = 0.693427
Epoch 29
Loss = 8.2689e-03, PNorm = 43.9362, GNorm = 2.4702, lr_0 = 9.6376e-04
Validation auc = 0.698592
Epoch 30
Validation auc = 0.692488
Epoch 31
Validation auc = 0.678404
Epoch 32
Validation auc = 0.674648
Epoch 33
Validation auc = 0.691080
Epoch 34
Loss = 6.4201e-03, PNorm = 43.9876, GNorm = 2.5990, lr_0 = 9.5552e-04
Validation auc = 0.702817
Epoch 35
Validation auc = 0.714554
Epoch 36
Validation auc = 0.718310
Epoch 37
Validation auc = 0.720188
Epoch 38
Validation auc = 0.728169
Epoch 39
Loss = 7.7628e-03, PNorm = 44.0446, GNorm = 2.3309, lr_0 = 9.4735e-04
Validation auc = 0.722535
Epoch 40
Validation auc = 0.703286
Epoch 41
Validation auc = 0.692958
Epoch 42
Validation auc = 0.698122
Epoch 43
Validation auc = 0.699531
Epoch 44
Loss = 7.2180e-03, PNorm = 44.1003, GNorm = 1.7805, lr_0 = 9.3925e-04
Validation auc = 0.702347
Epoch 45
Validation auc = 0.707981
Epoch 46
Validation auc = 0.713615
Epoch 47
Validation auc = 0.719249
Epoch 48
Validation auc = 0.714085
Epoch 49
Loss = 6.5047e-03, PNorm = 44.1625, GNorm = 1.7015, lr_0 = 9.3122e-04
Validation auc = 0.714554
Epoch 50
Validation auc = 0.709390
Epoch 51
Validation auc = 0.706103
Epoch 52
Validation auc = 0.705634
Epoch 53
Validation auc = 0.705634
Epoch 54
Loss = 7.2111e-03, PNorm = 44.2275, GNorm = 1.7031, lr_0 = 9.2326e-04
Validation auc = 0.696244
Epoch 55
Validation auc = 0.690610
Epoch 56
Validation auc = 0.687793
Epoch 57
Validation auc = 0.685915
Epoch 58
Validation auc = 0.686854
Epoch 59
Loss = 6.7776e-03, PNorm = 44.2997, GNorm = 1.9386, lr_0 = 9.1537e-04
Validation auc = 0.689202
Epoch 60
Validation auc = 0.691549
Epoch 61
Validation auc = 0.697183
Epoch 62
Validation auc = 0.701408
Epoch 63
Validation auc = 0.704695
Epoch 64
Loss = 4.3430e-03, PNorm = 44.3923, GNorm = 1.4096, lr_0 = 9.0754e-04
Validation auc = 0.710329
Epoch 65
Validation auc = 0.714554
Epoch 66
Validation auc = 0.707981
Epoch 67
Validation auc = 0.684038
Epoch 68
Validation auc = 0.688263
Epoch 69
Loss = 5.2218e-03, PNorm = 44.4923, GNorm = 1.3339, lr_0 = 8.9978e-04
Validation auc = 0.689671
Epoch 70
Validation auc = 0.679812
Epoch 71
Validation auc = 0.678404
Epoch 72
Validation auc = 0.670423
Epoch 73
Validation auc = 0.671831
Epoch 74
Loss = 5.6032e-03, PNorm = 44.6002, GNorm = 1.7707, lr_0 = 8.9209e-04
Validation auc = 0.679343
Epoch 75
Validation auc = 0.686854
Epoch 76
Validation auc = 0.705164
Epoch 77
Validation auc = 0.720657
Epoch 78
Validation auc = 0.723005
Epoch 79
Loss = 4.7687e-03, PNorm = 44.7039, GNorm = 2.0570, lr_0 = 8.8447e-04
Validation auc = 0.725352
Epoch 80
Validation auc = 0.729108
Epoch 81
Validation auc = 0.728169
Epoch 82
Validation auc = 0.723944
Epoch 83
Validation auc = 0.715023
Epoch 84
Loss = 4.2861e-03, PNorm = 44.8162, GNorm = 1.5919, lr_0 = 8.7691e-04
Validation auc = 0.707042
Epoch 85
Validation auc = 0.706103
Epoch 86
Validation auc = 0.711737
Epoch 87
Validation auc = 0.725352
Epoch 88
Validation auc = 0.728638
Epoch 89
Loss = 4.4490e-03, PNorm = 44.9109, GNorm = 0.8483, lr_0 = 8.6941e-04
Validation auc = 0.725352
Epoch 90
Validation auc = 0.723474
Epoch 91
Validation auc = 0.719718
Epoch 92
Validation auc = 0.721127
Epoch 93
Validation auc = 0.714085
Epoch 94
Loss = 5.8669e-03, PNorm = 45.0113, GNorm = 1.7277, lr_0 = 8.6198e-04
Validation auc = 0.706573
Epoch 95
Validation auc = 0.712207
Epoch 96
Validation auc = 0.711268
Epoch 97
Validation auc = 0.712207
Epoch 98
Validation auc = 0.725822
Epoch 99
Loss = 3.5424e-03, PNorm = 45.0927, GNorm = 1.0819, lr_0 = 8.5461e-04
Validation auc = 0.735211
Epoch 100
Validation auc = 0.744131
Epoch 101
Validation auc = 0.746479
Epoch 102
Validation auc = 0.749296
Epoch 103
Validation auc = 0.749296
Epoch 104
Loss = 4.8694e-03, PNorm = 45.1993, GNorm = 1.7179, lr_0 = 8.4730e-04
Validation auc = 0.742254
Epoch 105
Validation auc = 0.728169
Epoch 106
Validation auc = 0.723474
Epoch 107
Validation auc = 0.722066
Epoch 108
Validation auc = 0.730047
Epoch 109
Loss = 3.9114e-03, PNorm = 45.3027, GNorm = 1.8223, lr_0 = 8.4006e-04
Validation auc = 0.736150
Epoch 110
Validation auc = 0.745070
Epoch 111
Validation auc = 0.747887
Epoch 112
Validation auc = 0.744601
Epoch 113
Validation auc = 0.744131
Epoch 114
Loss = 5.8653e-03, PNorm = 45.4084, GNorm = 0.9567, lr_0 = 8.3288e-04
Validation auc = 0.745070
Epoch 115
Validation auc = 0.745070
Epoch 116
Validation auc = 0.744131
Epoch 117
Validation auc = 0.735681
Epoch 118
Validation auc = 0.727230
Epoch 119
Loss = 3.7882e-03, PNorm = 45.5228, GNorm = 1.6474, lr_0 = 8.2576e-04
Validation auc = 0.722535
Epoch 120
Validation auc = 0.707512
Epoch 121
Validation auc = 0.706573
Epoch 122
Validation auc = 0.702347
Epoch 123
Validation auc = 0.703756
Epoch 124
Loss = 4.5820e-03, PNorm = 45.6411, GNorm = 2.5159, lr_0 = 8.1870e-04
Validation auc = 0.696714
Epoch 125
Validation auc = 0.692019
Epoch 126
Validation auc = 0.702817
Epoch 127
Validation auc = 0.714554
Epoch 128
Validation auc = 0.715962
Epoch 129
Loss = 2.6547e-03, PNorm = 45.7501, GNorm = 1.1567, lr_0 = 8.1170e-04
Validation auc = 0.722535
Epoch 130
Validation auc = 0.729108
Epoch 131
Validation auc = 0.740845
Epoch 132
Validation auc = 0.744601
Epoch 133
Validation auc = 0.747887
Epoch 134
Loss = 3.0381e-03, PNorm = 45.8696, GNorm = 2.4095, lr_0 = 8.0476e-04
Validation auc = 0.751643
Epoch 135
Validation auc = 0.757746
Epoch 136
Validation auc = 0.747887
Epoch 137
Validation auc = 0.730516
Epoch 138
Validation auc = 0.725352
Epoch 139
Loss = 3.9470e-03, PNorm = 45.9819, GNorm = 1.4955, lr_0 = 7.9788e-04
Validation auc = 0.729577
Epoch 140
Validation auc = 0.726761
Epoch 141
Validation auc = 0.710798
Epoch 142
Validation auc = 0.704225
Epoch 143
Validation auc = 0.703286
Epoch 144
Loss = 5.8744e-03, PNorm = 46.1022, GNorm = 5.8748, lr_0 = 7.9106e-04
Validation auc = 0.708451
Epoch 145
Validation auc = 0.720188
Epoch 146
Validation auc = 0.734742
Epoch 147
Validation auc = 0.746009
Epoch 148
Validation auc = 0.753052
Epoch 149
Loss = 2.3966e-03, PNorm = 46.2263, GNorm = 1.9116, lr_0 = 7.8430e-04
Validation auc = 0.753052
Epoch 150
Validation auc = 0.753052
Epoch 151
Validation auc = 0.747887
Epoch 152
Validation auc = 0.748357
Epoch 153
Validation auc = 0.751643
Epoch 154
Loss = 3.5546e-03, PNorm = 46.3486, GNorm = 2.6340, lr_0 = 7.7759e-04
Validation auc = 0.726291
Epoch 155
Validation auc = 0.692488
Epoch 156
Validation auc = 0.692019
Epoch 157
Validation auc = 0.723474
Epoch 158
Validation auc = 0.730047
Epoch 159
Loss = 1.9263e-03, PNorm = 46.4365, GNorm = 0.9525, lr_0 = 7.7095e-04
Validation auc = 0.731455
Epoch 160
Validation auc = 0.729577
Epoch 161
Validation auc = 0.727230
Epoch 162
Validation auc = 0.729108
Epoch 163
Validation auc = 0.719249
Epoch 164
Loss = 3.7899e-03, PNorm = 46.5526, GNorm = 2.3258, lr_0 = 7.6436e-04
Validation auc = 0.704695
Epoch 165
Validation auc = 0.684977
Epoch 166
Validation auc = 0.686854
Epoch 167
Validation auc = 0.705634
Epoch 168
Validation auc = 0.729108
Epoch 169
Loss = 2.0820e-03, PNorm = 46.6589, GNorm = 0.9726, lr_0 = 7.5782e-04
Validation auc = 0.734742
Epoch 170
Validation auc = 0.735211
Epoch 171
Validation auc = 0.737089
Epoch 172
Validation auc = 0.735211
Epoch 173
Validation auc = 0.730516
Epoch 174
Loss = 2.9554e-03, PNorm = 46.7559, GNorm = 0.6721, lr_0 = 7.5134e-04
Validation auc = 0.723474
Epoch 175
Validation auc = 0.720188
Epoch 176
Validation auc = 0.727700
Epoch 177
Validation auc = 0.718779
Epoch 178
Validation auc = 0.708920
Epoch 179
Loss = 3.7678e-03, PNorm = 46.8399, GNorm = 2.6028, lr_0 = 7.4492e-04
Validation auc = 0.710798
Epoch 180
Validation auc = 0.714085
Epoch 181
Validation auc = 0.711268
Epoch 182
Validation auc = 0.712676
Epoch 183
Validation auc = 0.710798
Epoch 184
Loss = 2.2997e-03, PNorm = 46.9329, GNorm = 1.9824, lr_0 = 7.3855e-04
Validation auc = 0.715962
Epoch 185
Validation auc = 0.728638
Epoch 186
Validation auc = 0.731925
Epoch 187
Validation auc = 0.718310
Epoch 188
Validation auc = 0.699531
Epoch 189
Loss = 2.6309e-03, PNorm = 47.0298, GNorm = 2.2596, lr_0 = 7.3224e-04
Validation auc = 0.692488
Epoch 190
Validation auc = 0.703756
Epoch 191
Validation auc = 0.708920
Epoch 192
Validation auc = 0.707512
Epoch 193
Validation auc = 0.700469
Epoch 194
Loss = 2.2346e-03, PNorm = 47.1319, GNorm = 0.9901, lr_0 = 7.2598e-04
Validation auc = 0.695775
Epoch 195
Validation auc = 0.695305
Epoch 196
Validation auc = 0.699061
Epoch 197
Validation auc = 0.705164
Epoch 198
Validation auc = 0.707512
Epoch 199
Loss = 1.9787e-03, PNorm = 47.2301, GNorm = 1.0844, lr_0 = 7.1977e-04
Validation auc = 0.706573
Epoch 200
Validation auc = 0.701878
Epoch 201
Validation auc = 0.706103
Epoch 202
Validation auc = 0.713615
Epoch 203
Validation auc = 0.716901
Epoch 204
Loss = 1.7105e-03, PNorm = 47.3265, GNorm = 1.5676, lr_0 = 7.1362e-04
Validation auc = 0.717371
Epoch 205
Validation auc = 0.711737
Epoch 206
Validation auc = 0.713146
Epoch 207
Validation auc = 0.723944
Epoch 208
Validation auc = 0.733803
Epoch 209
Loss = 1.2667e-03, PNorm = 47.4004, GNorm = 1.1080, lr_0 = 7.0752e-04
Validation auc = 0.736620
Epoch 210
Validation auc = 0.730986
Epoch 211
Validation auc = 0.726291
Epoch 212
Validation auc = 0.717371
Epoch 213
Validation auc = 0.712207
Epoch 214
Loss = 1.2859e-03, PNorm = 47.4716, GNorm = 1.2173, lr_0 = 7.0147e-04
Validation auc = 0.706103
Epoch 215
Validation auc = 0.706103
Epoch 216
Validation auc = 0.715962
Epoch 217
Validation auc = 0.723944
Epoch 218
Validation auc = 0.724413
Epoch 219
Loss = 1.2577e-03, PNorm = 47.5442, GNorm = 0.8651, lr_0 = 6.9548e-04
Validation auc = 0.721596
Epoch 220
Validation auc = 0.716901
Epoch 221
Validation auc = 0.715493
Epoch 222
Validation auc = 0.720188
Epoch 223
Validation auc = 0.725822
Epoch 224
Loss = 3.2564e-03, PNorm = 47.6221, GNorm = 4.6161, lr_0 = 6.8953e-04
Validation auc = 0.721596
Epoch 225
Validation auc = 0.718310
Epoch 226
Validation auc = 0.719718
Epoch 227
Validation auc = 0.738967
Epoch 228
Validation auc = 0.742723
Epoch 229
Loss = 1.8788e-03, PNorm = 47.7110, GNorm = 1.4350, lr_0 = 6.8364e-04
Validation auc = 0.746948
Epoch 230
Validation auc = 0.745540
Epoch 231
Validation auc = 0.743192
Epoch 232
Validation auc = 0.746009
Epoch 233
Validation auc = 0.746009
Epoch 234
Loss = 7.9461e-04, PNorm = 47.7893, GNorm = 0.8181, lr_0 = 6.7779e-04
Validation auc = 0.748826
Epoch 235
Validation auc = 0.749296
Epoch 236
Validation auc = 0.747887
Epoch 237
Validation auc = 0.740376
Epoch 238
Validation auc = 0.733803
Epoch 239
Loss = 1.2991e-03, PNorm = 47.8684, GNorm = 0.5860, lr_0 = 6.7200e-04
Validation auc = 0.726291
Epoch 240
Validation auc = 0.717371
Epoch 241
Validation auc = 0.714085
Epoch 242
Validation auc = 0.709390
Epoch 243
Validation auc = 0.704695
Epoch 244
Loss = 7.5345e-04, PNorm = 47.9572, GNorm = 1.8425, lr_0 = 6.6625e-04
Validation auc = 0.711737
Epoch 245
Validation auc = 0.711737
Epoch 246
Validation auc = 0.707981
Epoch 247
Validation auc = 0.709390
Epoch 248
Validation auc = 0.710329
Epoch 249
Loss = 1.6357e-03, PNorm = 48.0291, GNorm = 2.0740, lr_0 = 6.6056e-04
Validation auc = 0.711268
Epoch 250
Validation auc = 0.707042
Epoch 251
Validation auc = 0.702347
Epoch 252
Validation auc = 0.701878
Epoch 253
Validation auc = 0.705164
Epoch 254
Loss = 9.7179e-04, PNorm = 48.0808, GNorm = 0.9920, lr_0 = 6.5491e-04
Validation auc = 0.712207
Epoch 255
Validation auc = 0.715023
Epoch 256
Validation auc = 0.714085
Epoch 257
Validation auc = 0.709390
Epoch 258
Validation auc = 0.708920
Epoch 259
Loss = 6.9867e-04, PNorm = 48.1329, GNorm = 0.9610, lr_0 = 6.4931e-04
Validation auc = 0.711737
Epoch 260
Validation auc = 0.715023
Epoch 261
Validation auc = 0.711737
Epoch 262
Validation auc = 0.707512
Epoch 263
Validation auc = 0.706103
Epoch 264
Loss = 2.9734e-03, PNorm = 48.1748, GNorm = 2.9093, lr_0 = 6.4376e-04
Validation auc = 0.705634
Epoch 265
Validation auc = 0.709390
Epoch 266
Validation auc = 0.711268
Epoch 267
Validation auc = 0.713146
Epoch 268
Validation auc = 0.715023
Epoch 269
Loss = 8.6538e-04, PNorm = 48.2203, GNorm = 0.5061, lr_0 = 6.3826e-04
Validation auc = 0.717840
Epoch 270
Validation auc = 0.717371
Epoch 271
Validation auc = 0.715023
Epoch 272
Validation auc = 0.709859
Epoch 273
Validation auc = 0.712207
Epoch 274
Loss = 5.3438e-04, PNorm = 48.2620, GNorm = 0.3126, lr_0 = 6.3280e-04
Validation auc = 0.716432
Epoch 275
Validation auc = 0.723474
Epoch 276
Validation auc = 0.726291
Epoch 277
Validation auc = 0.723944
Epoch 278
Validation auc = 0.727230
Epoch 279
Loss = 6.2545e-04, PNorm = 48.2997, GNorm = 0.5140, lr_0 = 6.2739e-04
Validation auc = 0.728169
Epoch 280
Validation auc = 0.730516
Epoch 281
Validation auc = 0.735211
Epoch 282
Validation auc = 0.736620
Epoch 283
Validation auc = 0.737089
Epoch 284
Loss = 3.2491e-04, PNorm = 48.3392, GNorm = 0.2721, lr_0 = 6.2203e-04
Validation auc = 0.731455
Epoch 285
Validation auc = 0.722535
Epoch 286
Validation auc = 0.712207
Epoch 287
Validation auc = 0.709390
Epoch 288
Validation auc = 0.704225
Epoch 289
Loss = 2.1811e-04, PNorm = 48.3899, GNorm = 0.3400, lr_0 = 6.1671e-04
Validation auc = 0.700939
Epoch 290
Validation auc = 0.699531
Epoch 291
Validation auc = 0.700469
Epoch 292
Validation auc = 0.703756
Epoch 293
Validation auc = 0.709859
Epoch 294
Loss = 1.2601e-03, PNorm = 48.4330, GNorm = 1.3351, lr_0 = 6.1144e-04
Validation auc = 0.716901
Epoch 295
Validation auc = 0.714554
Epoch 296
Validation auc = 0.711737
Epoch 297
Validation auc = 0.709859
Epoch 298
Validation auc = 0.707981
Epoch 299
Loss = 1.9659e-03, PNorm = 48.4778, GNorm = 1.7999, lr_0 = 6.0621e-04
Validation auc = 0.712676
Model 0 best validation auc = 0.807042 on epoch 5
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.912101
Ensemble test auc = 0.912101
Fold 1
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': 300,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': 1,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_1',
 'save_smiles_splits': False,
 'seed': 1,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': ['sars_cov_two_cl_protease_active'],
 'test': False,
 'test_fold_index': None,
 'train_data_size': 485,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 1
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.748357
Best score so far is 0.748357 at epoch 0 
Epoch 1
Validation auc = 0.758685
Best score so far is 0.758685 at epoch 1 
Epoch 2
Validation auc = 0.777934
Best score so far is 0.777934 at epoch 2 
Epoch 3
Validation auc = 0.782629
Best score so far is 0.782629 at epoch 3 
Epoch 4
Loss = 1.3281e-02, PNorm = 43.6395, GNorm = 3.3057, lr_0 = 6.5000e-04
Validation auc = 0.780751
Epoch 5
Validation auc = 0.786854
Best score so far is 0.786854 at epoch 5 
Epoch 6
Validation auc = 0.784038
Epoch 7
Validation auc = 0.788732
Best score so far is 0.788732 at epoch 7 
Epoch 8
Validation auc = 0.778873
Epoch 9
Loss = 1.2341e-02, PNorm = 43.6979, GNorm = 3.1745, lr_0 = 9.9743e-04
Validation auc = 0.770423
Epoch 10
Validation auc = 0.734742
Epoch 11
Validation auc = 0.721127
Epoch 12
Validation auc = 0.730516
Epoch 13
Validation auc = 0.743192
Epoch 14
Loss = 1.0239e-02, PNorm = 43.7676, GNorm = 2.9662, lr_0 = 9.8890e-04
Validation auc = 0.743662
Epoch 15
Validation auc = 0.749765
Epoch 16
Validation auc = 0.763850
Epoch 17
Validation auc = 0.750235
Epoch 18
Validation auc = 0.724883
Epoch 19
Loss = 7.6019e-03, PNorm = 43.8350, GNorm = 2.5069, lr_0 = 9.8045e-04
Validation auc = 0.724413
Epoch 20
Validation auc = 0.748826
Epoch 21
Validation auc = 0.767136
Epoch 22
Validation auc = 0.773709
Epoch 23
Validation auc = 0.781690
Epoch 24
Loss = 9.5392e-03, PNorm = 43.8933, GNorm = 3.3188, lr_0 = 9.7207e-04
Validation auc = 0.777934
Epoch 25
Validation auc = 0.763850
Epoch 26
Validation auc = 0.750704
Epoch 27
Validation auc = 0.732394
Epoch 28
Validation auc = 0.711268
Epoch 29
Loss = 8.7284e-03, PNorm = 43.9456, GNorm = 1.9837, lr_0 = 9.6376e-04
Validation auc = 0.707042
Epoch 30
Validation auc = 0.711268
Epoch 31
Validation auc = 0.723944
Epoch 32
Validation auc = 0.731455
Epoch 33
Validation auc = 0.737089
Epoch 34
Loss = 7.2765e-03, PNorm = 44.0017, GNorm = 1.8139, lr_0 = 9.5552e-04
Validation auc = 0.742254
Epoch 35
Validation auc = 0.745070
Epoch 36
Validation auc = 0.740845
Epoch 37
Validation auc = 0.737089
Epoch 38
Validation auc = 0.735211
Epoch 39
Loss = 9.0419e-03, PNorm = 44.0668, GNorm = 2.3596, lr_0 = 9.4735e-04
Validation auc = 0.726761
Epoch 40
Validation auc = 0.717840
Epoch 41
Validation auc = 0.710798
Epoch 42
Validation auc = 0.696244
Epoch 43
Validation auc = 0.693427
Epoch 44
Loss = 7.2950e-03, PNorm = 44.1404, GNorm = 1.1844, lr_0 = 9.3925e-04
Validation auc = 0.707981
Epoch 45
Validation auc = 0.716901
Epoch 46
Validation auc = 0.722066
Epoch 47
Validation auc = 0.719718
Epoch 48
Validation auc = 0.714554
Epoch 49
Loss = 7.6242e-03, PNorm = 44.2112, GNorm = 1.6601, lr_0 = 9.3122e-04
Validation auc = 0.707042
Epoch 50
Validation auc = 0.703286
Epoch 51
Validation auc = 0.705164
Epoch 52
Validation auc = 0.708451
Epoch 53
Validation auc = 0.713146
Epoch 54
Loss = 7.6492e-03, PNorm = 44.2890, GNorm = 2.5402, lr_0 = 9.2326e-04
Validation auc = 0.699061
Epoch 55
Validation auc = 0.688732
Epoch 56
Validation auc = 0.671831
Epoch 57
Validation auc = 0.666197
Epoch 58
Validation auc = 0.676526
Epoch 59
Loss = 5.4282e-03, PNorm = 44.3791, GNorm = 1.6666, lr_0 = 9.1537e-04
Validation auc = 0.676995
Epoch 60
Validation auc = 0.686854
Epoch 61
Validation auc = 0.696714
Epoch 62
Validation auc = 0.701878
Epoch 63
Validation auc = 0.703286
Epoch 64
Loss = 5.9677e-03, PNorm = 44.4763, GNorm = 2.9120, lr_0 = 9.0754e-04
Validation auc = 0.711268
Epoch 65
Validation auc = 0.721127
Epoch 66
Validation auc = 0.725352
Epoch 67
Validation auc = 0.726291
Epoch 68
Validation auc = 0.727700
Epoch 69
Loss = 5.5014e-03, PNorm = 44.5657, GNorm = 3.0543, lr_0 = 8.9978e-04
Validation auc = 0.726291
Epoch 70
Validation auc = 0.718779
Epoch 71
Validation auc = 0.723474
Epoch 72
Validation auc = 0.722535
Epoch 73
Validation auc = 0.725352
Epoch 74
Loss = 5.7510e-03, PNorm = 44.6566, GNorm = 1.8828, lr_0 = 8.9209e-04
Validation auc = 0.730986
Epoch 75
Validation auc = 0.740845
Epoch 76
Validation auc = 0.744601
Epoch 77
Validation auc = 0.732394
Epoch 78
Validation auc = 0.722066
Epoch 79
Loss = 4.1162e-03, PNorm = 44.7561, GNorm = 1.4165, lr_0 = 8.8447e-04
Validation auc = 0.724413
Epoch 80
Validation auc = 0.727230
Epoch 81
Validation auc = 0.727230
Epoch 82
Validation auc = 0.729577
Epoch 83
Validation auc = 0.729108
Epoch 84
Loss = 4.0396e-03, PNorm = 44.8595, GNorm = 3.3659, lr_0 = 8.7691e-04
Validation auc = 0.734272
Epoch 85
Validation auc = 0.746479
Epoch 86
Validation auc = 0.751174
Epoch 87
Validation auc = 0.749296
Epoch 88
Validation auc = 0.728638
Epoch 89
Loss = 6.0911e-03, PNorm = 44.9648, GNorm = 2.7539, lr_0 = 8.6941e-04
Validation auc = 0.717371
Epoch 90
Validation auc = 0.711268
Epoch 91
Validation auc = 0.715493
Epoch 92
Validation auc = 0.727700
Epoch 93
Validation auc = 0.723005
Epoch 94
Loss = 5.0094e-03, PNorm = 45.0647, GNorm = 1.4891, lr_0 = 8.6198e-04
Validation auc = 0.719718
Epoch 95
Validation auc = 0.720657
Epoch 96
Validation auc = 0.726291
Epoch 97
Validation auc = 0.727230
Epoch 98
Validation auc = 0.734742
Epoch 99
Loss = 3.2307e-03, PNorm = 45.1736, GNorm = 1.3052, lr_0 = 8.5461e-04
Validation auc = 0.740845
Epoch 100
Validation auc = 0.745070
Epoch 101
Validation auc = 0.748826
Epoch 102
Validation auc = 0.752582
Epoch 103
Validation auc = 0.748826
Epoch 104
Loss = 3.5872e-03, PNorm = 45.2916, GNorm = 1.3882, lr_0 = 8.4730e-04
Validation auc = 0.743662
Epoch 105
Validation auc = 0.736150
Epoch 106
Validation auc = 0.720188
Epoch 107
Validation auc = 0.727230
Epoch 108
Validation auc = 0.727230
Epoch 109
Loss = 3.6489e-03, PNorm = 45.4110, GNorm = 1.9646, lr_0 = 8.4006e-04
Validation auc = 0.723005
Epoch 110
Validation auc = 0.730047
Epoch 111
Validation auc = 0.732394
Epoch 112
Validation auc = 0.732864
Epoch 113
Validation auc = 0.724883
Epoch 114
Loss = 3.2533e-03, PNorm = 45.5253, GNorm = 1.6622, lr_0 = 8.3288e-04
Validation auc = 0.719249
Epoch 115
Validation auc = 0.715023
Epoch 116
Validation auc = 0.722066
Epoch 117
Validation auc = 0.718779
Epoch 118
Validation auc = 0.714554
Epoch 119
Loss = 4.8318e-03, PNorm = 45.6565, GNorm = 3.6518, lr_0 = 8.2576e-04
Validation auc = 0.715023
Epoch 120
Validation auc = 0.720657
Epoch 121
Validation auc = 0.715493
Epoch 122
Validation auc = 0.709390
Epoch 123
Validation auc = 0.714554
Epoch 124
Loss = 2.6203e-03, PNorm = 45.7757, GNorm = 2.1391, lr_0 = 8.1870e-04
Validation auc = 0.710329
Epoch 125
Validation auc = 0.703756
Epoch 126
Validation auc = 0.697183
Epoch 127
Validation auc = 0.704695
Epoch 128
Validation auc = 0.713146
Epoch 129
Loss = 2.5124e-03, PNorm = 45.8940, GNorm = 1.2549, lr_0 = 8.1170e-04
Validation auc = 0.711268
Epoch 130
Validation auc = 0.711268
Epoch 131
Validation auc = 0.713615
Epoch 132
Validation auc = 0.717371
Epoch 133
Validation auc = 0.717371
Epoch 134
Loss = 4.3244e-03, PNorm = 46.0090, GNorm = 1.4106, lr_0 = 8.0476e-04
Validation auc = 0.712207
Epoch 135
Validation auc = 0.714085
Epoch 136
Validation auc = 0.709859
Epoch 137
Validation auc = 0.707042
Epoch 138
Validation auc = 0.698122
Epoch 139
Loss = 1.3710e-03, PNorm = 46.1118, GNorm = 0.5171, lr_0 = 7.9788e-04
Validation auc = 0.699061
Epoch 140
Validation auc = 0.712676
Epoch 141
Validation auc = 0.719249
Epoch 142
Validation auc = 0.717840
Epoch 143
Validation auc = 0.718310
Epoch 144
Loss = 4.6545e-03, PNorm = 46.2181, GNorm = 2.6318, lr_0 = 7.9106e-04
Validation auc = 0.722066
Epoch 145
Validation auc = 0.728638
Epoch 146
Validation auc = 0.718310
Epoch 147
Validation auc = 0.726291
Epoch 148
Validation auc = 0.732394
Epoch 149
Loss = 3.0755e-03, PNorm = 46.3303, GNorm = 3.0063, lr_0 = 7.8430e-04
Validation auc = 0.727230
Epoch 150
Validation auc = 0.715962
Epoch 151
Validation auc = 0.708920
Epoch 152
Validation auc = 0.700469
Epoch 153
Validation auc = 0.705164
Epoch 154
Loss = 1.7648e-03, PNorm = 46.4597, GNorm = 1.0529, lr_0 = 7.7759e-04
Validation auc = 0.700939
Epoch 155
Validation auc = 0.698122
Epoch 156
Validation auc = 0.701408
Epoch 157
Validation auc = 0.710329
Epoch 158
Validation auc = 0.715023
Epoch 159
Loss = 2.2577e-03, PNorm = 46.5410, GNorm = 1.7510, lr_0 = 7.7095e-04
Validation auc = 0.715962
Epoch 160
Validation auc = 0.720188
Epoch 161
Validation auc = 0.732394
Epoch 162
Validation auc = 0.730516
Epoch 163
Validation auc = 0.723474
Epoch 164
Loss = 3.7335e-03, PNorm = 46.6357, GNorm = 3.6544, lr_0 = 7.6436e-04
Validation auc = 0.721127
Epoch 165
Validation auc = 0.718310
Epoch 166
Validation auc = 0.717371
Epoch 167
Validation auc = 0.713146
Epoch 168
Validation auc = 0.708451
Epoch 169
Loss = 2.1102e-03, PNorm = 46.7392, GNorm = 0.5235, lr_0 = 7.5782e-04
Validation auc = 0.706573
Epoch 170
Validation auc = 0.703286
Epoch 171
Validation auc = 0.707042
Epoch 172
Validation auc = 0.710329
Epoch 173
Validation auc = 0.709859
Epoch 174
Loss = 1.7953e-03, PNorm = 46.8278, GNorm = 1.2115, lr_0 = 7.5134e-04
Validation auc = 0.707981
Epoch 175
Validation auc = 0.708451
Epoch 176
Validation auc = 0.712207
Epoch 177
Validation auc = 0.706573
Epoch 178
Validation auc = 0.706103
Epoch 179
Loss = 2.3043e-03, PNorm = 46.9219, GNorm = 0.9040, lr_0 = 7.4492e-04
Validation auc = 0.709390
Epoch 180
Validation auc = 0.703756
Epoch 181
Validation auc = 0.707042
Epoch 182
Validation auc = 0.703756
Epoch 183
Validation auc = 0.705164
Epoch 184
Loss = 1.1782e-03, PNorm = 46.9982, GNorm = 0.9985, lr_0 = 7.3855e-04
Validation auc = 0.702347
Epoch 185
Validation auc = 0.708920
Epoch 186
Validation auc = 0.707981
Epoch 187
Validation auc = 0.706103
Epoch 188
Validation auc = 0.705164
Epoch 189
Loss = 2.4576e-03, PNorm = 47.0822, GNorm = 2.3206, lr_0 = 7.3224e-04
Validation auc = 0.706103
Epoch 190
Validation auc = 0.707512
Epoch 191
Validation auc = 0.688732
Epoch 192
Validation auc = 0.690141
Epoch 193
Validation auc = 0.709390
Epoch 194
Loss = 1.7883e-03, PNorm = 47.1653, GNorm = 1.8212, lr_0 = 7.2598e-04
Validation auc = 0.712676
Epoch 195
Validation auc = 0.715023
Epoch 196
Validation auc = 0.717840
Epoch 197
Validation auc = 0.711737
Epoch 198
Validation auc = 0.704695
Epoch 199
Loss = 1.2778e-03, PNorm = 47.2472, GNorm = 0.1728, lr_0 = 7.1977e-04
Validation auc = 0.688732
Epoch 200
Validation auc = 0.679812
Epoch 201
Validation auc = 0.676995
Epoch 202
Validation auc = 0.673709
Epoch 203
Validation auc = 0.681690
Epoch 204
Loss = 1.8232e-03, PNorm = 47.3362, GNorm = 0.6235, lr_0 = 7.1362e-04
Validation auc = 0.704695
Epoch 205
Validation auc = 0.714554
Epoch 206
Validation auc = 0.718310
Epoch 207
Validation auc = 0.721127
Epoch 208
Validation auc = 0.726761
Epoch 209
Loss = 3.0984e-03, PNorm = 47.4257, GNorm = 1.0989, lr_0 = 7.0752e-04
Validation auc = 0.726761
Epoch 210
Validation auc = 0.730986
Epoch 211
Validation auc = 0.731925
Epoch 212
Validation auc = 0.728169
Epoch 213
Validation auc = 0.721596
Epoch 214
Loss = 1.3907e-03, PNorm = 47.5104, GNorm = 1.7164, lr_0 = 7.0147e-04
Validation auc = 0.720657
Epoch 215
Validation auc = 0.716432
Epoch 216
Validation auc = 0.710798
Epoch 217
Validation auc = 0.702817
Epoch 218
Validation auc = 0.701878
Epoch 219
Loss = 1.1220e-03, PNorm = 47.5787, GNorm = 1.2384, lr_0 = 6.9548e-04
Validation auc = 0.703756
Epoch 220
Validation auc = 0.703756
Epoch 221
Validation auc = 0.702347
Epoch 222
Validation auc = 0.709390
Epoch 223
Validation auc = 0.707042
Epoch 224
Loss = 1.2258e-03, PNorm = 47.6320, GNorm = 0.7692, lr_0 = 6.8953e-04
Validation auc = 0.706103
Epoch 225
Validation auc = 0.706573
Epoch 226
Validation auc = 0.707042
Epoch 227
Validation auc = 0.704225
Epoch 228
Validation auc = 0.702347
Epoch 229
Loss = 8.8232e-04, PNorm = 47.6865, GNorm = 0.7597, lr_0 = 6.8364e-04
Validation auc = 0.697183
Epoch 230
Validation auc = 0.694366
Epoch 231
Validation auc = 0.700469
Epoch 232
Validation auc = 0.702817
Epoch 233
Validation auc = 0.701408
Epoch 234
Loss = 1.2867e-03, PNorm = 47.7306, GNorm = 0.7795, lr_0 = 6.7779e-04
Validation auc = 0.701878
Epoch 235
Validation auc = 0.700000
Epoch 236
Validation auc = 0.705164
Epoch 237
Validation auc = 0.703756
Epoch 238
Validation auc = 0.701878
Epoch 239
Loss = 1.2096e-03, PNorm = 47.7817, GNorm = 0.9324, lr_0 = 6.7200e-04
Validation auc = 0.693897
Epoch 240
Validation auc = 0.700000
Epoch 241
Validation auc = 0.702817
Epoch 242
Validation auc = 0.694836
Epoch 243
Validation auc = 0.695775
Epoch 244
Loss = 1.3718e-03, PNorm = 47.8316, GNorm = 0.4984, lr_0 = 6.6625e-04
Validation auc = 0.698592
Epoch 245
Validation auc = 0.700000
Epoch 246
Validation auc = 0.697183
Epoch 247
Validation auc = 0.694366
Epoch 248
Validation auc = 0.693897
Epoch 249
Loss = 4.2921e-04, PNorm = 47.8980, GNorm = 0.4960, lr_0 = 6.6056e-04
Validation auc = 0.692488
Epoch 250
Validation auc = 0.694836
Epoch 251
Validation auc = 0.696244
Epoch 252
Validation auc = 0.692958
Epoch 253
Validation auc = 0.691080
Epoch 254
Loss = 2.0403e-04, PNorm = 47.9546, GNorm = 0.1713, lr_0 = 6.5491e-04
Validation auc = 0.690141
Epoch 255
Validation auc = 0.693427
Epoch 256
Validation auc = 0.701878
Epoch 257
Validation auc = 0.700469
Epoch 258
Validation auc = 0.705164
Epoch 259
Loss = 8.3747e-04, PNorm = 47.9975, GNorm = 0.9594, lr_0 = 6.4931e-04
Validation auc = 0.708920
Epoch 260
Validation auc = 0.712676
Epoch 261
Validation auc = 0.716901
Epoch 262
Validation auc = 0.714554
Epoch 263
Validation auc = 0.710329
Epoch 264
Loss = 1.0374e-03, PNorm = 48.0341, GNorm = 0.1132, lr_0 = 6.4376e-04
Validation auc = 0.707981
Epoch 265
Validation auc = 0.707981
Epoch 266
Validation auc = 0.704225
Epoch 267
Validation auc = 0.700000
Epoch 268
Validation auc = 0.700000
Epoch 269
Loss = 3.4881e-04, PNorm = 48.0777, GNorm = 0.2931, lr_0 = 6.3826e-04
Validation auc = 0.699061
Epoch 270
Validation auc = 0.705634
Epoch 271
Validation auc = 0.703286
Epoch 272
Validation auc = 0.702347
Epoch 273
Validation auc = 0.702817
Epoch 274
Loss = 6.5068e-04, PNorm = 48.1133, GNorm = 0.3369, lr_0 = 6.3280e-04
Validation auc = 0.698592
Epoch 275
Validation auc = 0.692958
Epoch 276
Validation auc = 0.692019
Epoch 277
Validation auc = 0.693897
Epoch 278
Validation auc = 0.697653
Epoch 279
Loss = 1.2326e-03, PNorm = 48.1536, GNorm = 3.4959, lr_0 = 6.2739e-04
Validation auc = 0.693427
Epoch 280
Validation auc = 0.684038
Epoch 281
Validation auc = 0.688732
Epoch 282
Validation auc = 0.699531
Epoch 283
Validation auc = 0.707512
Epoch 284
Loss = 4.6837e-04, PNorm = 48.1944, GNorm = 1.2111, lr_0 = 6.2203e-04
Validation auc = 0.709859
Epoch 285
Validation auc = 0.714554
Epoch 286
Validation auc = 0.715962
Epoch 287
Validation auc = 0.711268
Epoch 288
Validation auc = 0.708920
Epoch 289
Loss = 7.9909e-04, PNorm = 48.2522, GNorm = 1.3115, lr_0 = 6.1671e-04
Validation auc = 0.706103
Epoch 290
Validation auc = 0.704225
Epoch 291
Validation auc = 0.702817
Epoch 292
Validation auc = 0.696714
Epoch 293
Validation auc = 0.694836
Epoch 294
Loss = 3.3721e-04, PNorm = 48.3007, GNorm = 0.6610, lr_0 = 6.1144e-04
Validation auc = 0.686854
Epoch 295
Validation auc = 0.688732
Epoch 296
Validation auc = 0.687793
Epoch 297
Validation auc = 0.688732
Epoch 298
Validation auc = 0.688263
Epoch 299
Loss = 3.6565e-04, PNorm = 48.3322, GNorm = 0.9804, lr_0 = 6.0621e-04
Validation auc = 0.692019
Model 0 best validation auc = 0.788732 on epoch 7
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.872968
Ensemble test auc = 0.872968
Fold 2
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': 300,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': 1,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_2',
 'save_smiles_splits': False,
 'seed': 2,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': ['sars_cov_two_cl_protease_active'],
 'test': False,
 'test_fold_index': None,
 'train_data_size': 485,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 2
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.735681
Best score so far is 0.735681 at epoch 0 
Epoch 1
Validation auc = 0.753052
Best score so far is 0.753052 at epoch 1 
Epoch 2
Validation auc = 0.763380
Best score so far is 0.763380 at epoch 2 
Epoch 3
Validation auc = 0.779812
Best score so far is 0.779812 at epoch 3 
Epoch 4
Loss = 1.5464e-02, PNorm = 43.6382, GNorm = 3.0935, lr_0 = 6.5000e-04
Validation auc = 0.793897
Best score so far is 0.793897 at epoch 4 
Epoch 5
Validation auc = 0.803756
Best score so far is 0.803756 at epoch 5 
Epoch 6
Validation auc = 0.807042
Best score so far is 0.807042 at epoch 6 
Epoch 7
Validation auc = 0.802347
Epoch 8
Validation auc = 0.786385
Epoch 9
Loss = 1.2788e-02, PNorm = 43.6987, GNorm = 4.7032, lr_0 = 9.9743e-04
Validation auc = 0.778873
Epoch 10
Validation auc = 0.769484
Epoch 11
Validation auc = 0.766667
Epoch 12
Validation auc = 0.770423
Epoch 13
Validation auc = 0.777465
Epoch 14
Loss = 9.7583e-03, PNorm = 43.7671, GNorm = 2.7123, lr_0 = 9.8890e-04
Validation auc = 0.790610
Epoch 15
Validation auc = 0.786854
Epoch 16
Validation auc = 0.790610
Epoch 17
Validation auc = 0.796244
Epoch 18
Validation auc = 0.778873
Epoch 19
Loss = 7.6248e-03, PNorm = 43.8252, GNorm = 1.9837, lr_0 = 9.8045e-04
Validation auc = 0.757277
Epoch 20
Validation auc = 0.755399
Epoch 21
Validation auc = 0.761033
Epoch 22
Validation auc = 0.769484
Epoch 23
Validation auc = 0.759155
Epoch 24
Loss = 7.7209e-03, PNorm = 43.8797, GNorm = 2.4037, lr_0 = 9.7207e-04
Validation auc = 0.753991
Epoch 25
Validation auc = 0.754460
Epoch 26
Validation auc = 0.757746
Epoch 27
Validation auc = 0.753991
Epoch 28
Validation auc = 0.755399
Epoch 29
Loss = 9.8073e-03, PNorm = 43.9321, GNorm = 1.8169, lr_0 = 9.6376e-04
Validation auc = 0.733803
Epoch 30
Validation auc = 0.715962
Epoch 31
Validation auc = 0.695775
Epoch 32
Validation auc = 0.690141
Epoch 33
Validation auc = 0.694836
Epoch 34
Loss = 9.1678e-03, PNorm = 43.9834, GNorm = 2.6477, lr_0 = 9.5552e-04
Validation auc = 0.705634
Epoch 35
Validation auc = 0.718310
Epoch 36
Validation auc = 0.722066
Epoch 37
Validation auc = 0.731455
Epoch 38
Validation auc = 0.730986
Epoch 39
Loss = 7.2744e-03, PNorm = 44.0472, GNorm = 3.1513, lr_0 = 9.4735e-04
Validation auc = 0.729577
Epoch 40
Validation auc = 0.715493
Epoch 41
Validation auc = 0.714085
Epoch 42
Validation auc = 0.708451
Epoch 43
Validation auc = 0.702817
Epoch 44
Loss = 8.8688e-03, PNorm = 44.1195, GNorm = 2.5369, lr_0 = 9.3925e-04
Validation auc = 0.695305
Epoch 45
Validation auc = 0.699061
Epoch 46
Validation auc = 0.705634
Epoch 47
Validation auc = 0.709390
Epoch 48
Validation auc = 0.710798
Epoch 49
Loss = 6.9971e-03, PNorm = 44.1977, GNorm = 1.7457, lr_0 = 9.3122e-04
Validation auc = 0.716432
Epoch 50
Validation auc = 0.719249
Epoch 51
Validation auc = 0.722535
Epoch 52
Validation auc = 0.712676
Epoch 53
Validation auc = 0.698122
Epoch 54
Loss = 6.1779e-03, PNorm = 44.2725, GNorm = 2.1156, lr_0 = 9.2326e-04
Validation auc = 0.690610
Epoch 55
Validation auc = 0.684977
Epoch 56
Validation auc = 0.686854
Epoch 57
Validation auc = 0.692019
Epoch 58
Validation auc = 0.697183
Epoch 59
Loss = 7.4237e-03, PNorm = 44.3563, GNorm = 1.4896, lr_0 = 9.1537e-04
Validation auc = 0.698592
Epoch 60
Validation auc = 0.700000
Epoch 61
Validation auc = 0.692488
Epoch 62
Validation auc = 0.691080
Epoch 63
Validation auc = 0.698122
Epoch 64
Loss = 5.2718e-03, PNorm = 44.4425, GNorm = 1.7440, lr_0 = 9.0754e-04
Validation auc = 0.710329
Epoch 65
Validation auc = 0.720188
Epoch 66
Validation auc = 0.737559
Epoch 67
Validation auc = 0.742723
Epoch 68
Validation auc = 0.738028
Epoch 69
Loss = 4.4725e-03, PNorm = 44.5363, GNorm = 2.7894, lr_0 = 8.9978e-04
Validation auc = 0.738967
Epoch 70
Validation auc = 0.730047
Epoch 71
Validation auc = 0.707042
Epoch 72
Validation auc = 0.687324
Epoch 73
Validation auc = 0.693897
Epoch 74
Loss = 4.3506e-03, PNorm = 44.6492, GNorm = 3.0610, lr_0 = 8.9209e-04
Validation auc = 0.703756
Epoch 75
Validation auc = 0.703756
Epoch 76
Validation auc = 0.713146
Epoch 77
Validation auc = 0.721127
Epoch 78
Validation auc = 0.723944
Epoch 79
Loss = 6.7511e-03, PNorm = 44.7382, GNorm = 2.5255, lr_0 = 8.8447e-04
Validation auc = 0.721127
Epoch 80
Validation auc = 0.718310
Epoch 81
Validation auc = 0.717840
Epoch 82
Validation auc = 0.719718
Epoch 83
Validation auc = 0.723474
Epoch 84
Loss = 5.9936e-03, PNorm = 44.8333, GNorm = 1.9138, lr_0 = 8.7691e-04
Validation auc = 0.719718
Epoch 85
Validation auc = 0.717840
Epoch 86
Validation auc = 0.714085
Epoch 87
Validation auc = 0.723005
Epoch 88
Validation auc = 0.740376
Epoch 89
Loss = 6.3977e-03, PNorm = 44.9276, GNorm = 2.1061, lr_0 = 8.6941e-04
Validation auc = 0.747418
Epoch 90
Validation auc = 0.738967
Epoch 91
Validation auc = 0.741784
Epoch 92
Validation auc = 0.743662
Epoch 93
Validation auc = 0.749765
Epoch 94
Loss = 4.6013e-03, PNorm = 45.0386, GNorm = 1.7728, lr_0 = 8.6198e-04
Validation auc = 0.752582
Epoch 95
Validation auc = 0.752582
Epoch 96
Validation auc = 0.742254
Epoch 97
Validation auc = 0.732394
Epoch 98
Validation auc = 0.718779
Epoch 99
Loss = 6.0965e-03, PNorm = 45.1434, GNorm = 3.9454, lr_0 = 8.5461e-04
Validation auc = 0.717840
Epoch 100
Validation auc = 0.722535
Epoch 101
Validation auc = 0.725822
Epoch 102
Validation auc = 0.730516
Epoch 103
Validation auc = 0.739437
Epoch 104
Loss = 5.5108e-03, PNorm = 45.2461, GNorm = 1.6413, lr_0 = 8.4730e-04
Validation auc = 0.744601
Epoch 105
Validation auc = 0.739906
Epoch 106
Validation auc = 0.733333
Epoch 107
Validation auc = 0.727230
Epoch 108
Validation auc = 0.729108
Epoch 109
Loss = 4.9587e-03, PNorm = 45.3705, GNorm = 1.8581, lr_0 = 8.4006e-04
Validation auc = 0.723944
Epoch 110
Validation auc = 0.718310
Epoch 111
Validation auc = 0.725822
Epoch 112
Validation auc = 0.725352
Epoch 113
Validation auc = 0.722535
Epoch 114
Loss = 3.1552e-03, PNorm = 45.4906, GNorm = 1.8368, lr_0 = 8.3288e-04
Validation auc = 0.712676
Epoch 115
Validation auc = 0.722066
Epoch 116
Validation auc = 0.724883
Epoch 117
Validation auc = 0.727700
Epoch 118
Validation auc = 0.711737
Epoch 119
Loss = 4.7810e-03, PNorm = 45.5871, GNorm = 3.2167, lr_0 = 8.2576e-04
Validation auc = 0.703286
Epoch 120
Validation auc = 0.722535
Epoch 121
Validation auc = 0.735681
Epoch 122
Validation auc = 0.741784
Epoch 123
Validation auc = 0.747887
Epoch 124
Loss = 5.0233e-03, PNorm = 45.6960, GNorm = 1.3475, lr_0 = 8.1870e-04
Validation auc = 0.751643
Epoch 125
Validation auc = 0.753521
Epoch 126
Validation auc = 0.748826
Epoch 127
Validation auc = 0.741784
Epoch 128
Validation auc = 0.738967
Epoch 129
Loss = 2.2205e-03, PNorm = 45.8290, GNorm = 0.6286, lr_0 = 8.1170e-04
Validation auc = 0.729577
Epoch 130
Validation auc = 0.735211
Epoch 131
Validation auc = 0.739906
Epoch 132
Validation auc = 0.743662
Epoch 133
Validation auc = 0.744131
Epoch 134
Loss = 2.0977e-03, PNorm = 45.9229, GNorm = 0.8534, lr_0 = 8.0476e-04
Validation auc = 0.748826
Epoch 135
Validation auc = 0.753052
Epoch 136
Validation auc = 0.754460
Epoch 137
Validation auc = 0.749765
Epoch 138
Validation auc = 0.741315
Epoch 139
Loss = 3.1153e-03, PNorm = 46.0304, GNorm = 1.0333, lr_0 = 7.9788e-04
Validation auc = 0.726291
Epoch 140
Validation auc = 0.714554
Epoch 141
Validation auc = 0.701408
Epoch 142
Validation auc = 0.696244
Epoch 143
Validation auc = 0.692019
Epoch 144
Loss = 4.5610e-03, PNorm = 46.1347, GNorm = 1.8195, lr_0 = 7.9106e-04
Validation auc = 0.689202
Epoch 145
Validation auc = 0.695775
Epoch 146
Validation auc = 0.695305
Epoch 147
Validation auc = 0.705164
Epoch 148
Validation auc = 0.716901
Epoch 149
Loss = 2.3366e-03, PNorm = 46.2380, GNorm = 0.9573, lr_0 = 7.8430e-04
Validation auc = 0.728169
Epoch 150
Validation auc = 0.728638
Epoch 151
Validation auc = 0.731455
Epoch 152
Validation auc = 0.738967
Epoch 153
Validation auc = 0.742723
Epoch 154
Loss = 2.6059e-03, PNorm = 46.3473, GNorm = 1.0375, lr_0 = 7.7759e-04
Validation auc = 0.742254
Epoch 155
Validation auc = 0.740845
Epoch 156
Validation auc = 0.738028
Epoch 157
Validation auc = 0.729577
Epoch 158
Validation auc = 0.725352
Epoch 159
Loss = 2.4412e-03, PNorm = 46.4480, GNorm = 1.2678, lr_0 = 7.7095e-04
Validation auc = 0.724883
Epoch 160
Validation auc = 0.722535
Epoch 161
Validation auc = 0.714085
Epoch 162
Validation auc = 0.711268
Epoch 163
Validation auc = 0.716901
Epoch 164
Loss = 2.1988e-03, PNorm = 46.5385, GNorm = 1.2947, lr_0 = 7.6436e-04
Validation auc = 0.724883
Epoch 165
Validation auc = 0.727230
Epoch 166
Validation auc = 0.720657
Epoch 167
Validation auc = 0.721127
Epoch 168
Validation auc = 0.721596
Epoch 169
Loss = 2.8570e-03, PNorm = 46.6290, GNorm = 1.8495, lr_0 = 7.5782e-04
Validation auc = 0.720657
Epoch 170
Validation auc = 0.719249
Epoch 171
Validation auc = 0.723474
Epoch 172
Validation auc = 0.722535
Epoch 173
Validation auc = 0.723944
Epoch 174
Loss = 2.0409e-03, PNorm = 46.7276, GNorm = 0.7881, lr_0 = 7.5134e-04
Validation auc = 0.723944
Epoch 175
Validation auc = 0.712676
Epoch 176
Validation auc = 0.712207
Epoch 177
Validation auc = 0.714554
Epoch 178
Validation auc = 0.715962
Epoch 179
Loss = 2.7371e-03, PNorm = 46.8177, GNorm = 1.3976, lr_0 = 7.4492e-04
Validation auc = 0.698122
Epoch 180
Validation auc = 0.699061
Epoch 181
Validation auc = 0.707512
Epoch 182
Validation auc = 0.716432
Epoch 183
Validation auc = 0.724883
Epoch 184
Loss = 2.5370e-03, PNorm = 46.9012, GNorm = 0.7865, lr_0 = 7.3855e-04
Validation auc = 0.722066
Epoch 185
Validation auc = 0.713146
Epoch 186
Validation auc = 0.704695
Epoch 187
Validation auc = 0.698592
Epoch 188
Validation auc = 0.692019
Epoch 189
Loss = 1.5977e-03, PNorm = 46.9804, GNorm = 1.0324, lr_0 = 7.3224e-04
Validation auc = 0.686385
Epoch 190
Validation auc = 0.690610
Epoch 191
Validation auc = 0.686854
Epoch 192
Validation auc = 0.690141
Epoch 193
Validation auc = 0.699531
Epoch 194
Loss = 1.3972e-03, PNorm = 47.0599, GNorm = 1.2062, lr_0 = 7.2598e-04
Validation auc = 0.718310
Epoch 195
Validation auc = 0.724413
Epoch 196
Validation auc = 0.721127
Epoch 197
Validation auc = 0.719249
Epoch 198
Validation auc = 0.720657
Epoch 199
Loss = 1.0990e-03, PNorm = 47.1352, GNorm = 0.8278, lr_0 = 7.1977e-04
Validation auc = 0.726761
Epoch 200
Validation auc = 0.721596
Epoch 201
Validation auc = 0.715493
Epoch 202
Validation auc = 0.712676
Epoch 203
Validation auc = 0.715023
Epoch 204
Loss = 8.9090e-04, PNorm = 47.2135, GNorm = 1.0664, lr_0 = 7.1362e-04
Validation auc = 0.716432
Epoch 205
Validation auc = 0.717371
Epoch 206
Validation auc = 0.720657
Epoch 207
Validation auc = 0.725352
Epoch 208
Validation auc = 0.720188
Epoch 209
Loss = 2.8383e-03, PNorm = 47.2953, GNorm = 1.6609, lr_0 = 7.0752e-04
Validation auc = 0.735681
Epoch 210
Validation auc = 0.732864
Epoch 211
Validation auc = 0.731925
Epoch 212
Validation auc = 0.727700
Epoch 213
Validation auc = 0.721596
Epoch 214
Loss = 1.6405e-03, PNorm = 47.3525, GNorm = 1.4230, lr_0 = 7.0147e-04
Validation auc = 0.715493
Epoch 215
Validation auc = 0.707512
Epoch 216
Validation auc = 0.694366
Epoch 217
Validation auc = 0.679812
Epoch 218
Validation auc = 0.671831
Epoch 219
Loss = 2.9893e-03, PNorm = 47.4315, GNorm = 1.3884, lr_0 = 6.9548e-04
Validation auc = 0.682160
Epoch 220
Validation auc = 0.694836
Epoch 221
Validation auc = 0.702347
Epoch 222
Validation auc = 0.709390
Epoch 223
Validation auc = 0.711268
Epoch 224
Loss = 1.5379e-03, PNorm = 47.5052, GNorm = 1.7841, lr_0 = 6.8953e-04
Validation auc = 0.715493
Epoch 225
Validation auc = 0.723005
Epoch 226
Validation auc = 0.725822
Epoch 227
Validation auc = 0.719718
Epoch 228
Validation auc = 0.712676
Epoch 229
Loss = 1.7297e-03, PNorm = 47.5798, GNorm = 1.5355, lr_0 = 6.8364e-04
Validation auc = 0.716432
Epoch 230
Validation auc = 0.718310
Epoch 231
Validation auc = 0.716432
Epoch 232
Validation auc = 0.712676
Epoch 233
Validation auc = 0.710329
Epoch 234
Loss = 3.9758e-04, PNorm = 47.6518, GNorm = 0.5308, lr_0 = 6.7779e-04
Validation auc = 0.715023
Epoch 235
Validation auc = 0.722066
Epoch 236
Validation auc = 0.723944
Epoch 237
Validation auc = 0.716432
Epoch 238
Validation auc = 0.708451
Epoch 239
Loss = 2.7197e-03, PNorm = 47.7170, GNorm = 0.5089, lr_0 = 6.7200e-04
Validation auc = 0.700939
Epoch 240
Validation auc = 0.690610
Epoch 241
Validation auc = 0.687793
Epoch 242
Validation auc = 0.691549
Epoch 243
Validation auc = 0.692488
Epoch 244
Loss = 1.4397e-03, PNorm = 47.8040, GNorm = 0.9185, lr_0 = 6.6625e-04
Validation auc = 0.692488
Epoch 245
Validation auc = 0.694836
Epoch 246
Validation auc = 0.696244
Epoch 247
Validation auc = 0.699531
Epoch 248
Validation auc = 0.704695
Epoch 249
Loss = 9.1228e-04, PNorm = 47.8769, GNorm = 0.7364, lr_0 = 6.6056e-04
Validation auc = 0.708451
Epoch 250
Validation auc = 0.709390
Epoch 251
Validation auc = 0.709859
Epoch 252
Validation auc = 0.711268
Epoch 253
Validation auc = 0.700939
Epoch 254
Loss = 1.3426e-03, PNorm = 47.9443, GNorm = 1.0343, lr_0 = 6.5491e-04
Validation auc = 0.692019
Epoch 255
Validation auc = 0.688732
Epoch 256
Validation auc = 0.685446
Epoch 257
Validation auc = 0.685446
Epoch 258
Validation auc = 0.685915
Epoch 259
Loss = 2.4867e-04, PNorm = 48.0066, GNorm = 0.2739, lr_0 = 6.4931e-04
Validation auc = 0.684977
Epoch 260
Validation auc = 0.690610
Epoch 261
Validation auc = 0.690141
Epoch 262
Validation auc = 0.686385
Epoch 263
Validation auc = 0.682629
Epoch 264
Loss = 1.7090e-04, PNorm = 48.0587, GNorm = 0.3409, lr_0 = 6.4376e-04
Validation auc = 0.689202
Epoch 265
Validation auc = 0.691080
Epoch 266
Validation auc = 0.692488
Epoch 267
Validation auc = 0.689202
Epoch 268
Validation auc = 0.695305
Epoch 269
Loss = 2.2349e-03, PNorm = 48.1045, GNorm = 1.0708, lr_0 = 6.3826e-04
Validation auc = 0.707981
Epoch 270
Validation auc = 0.708920
Epoch 271
Validation auc = 0.710329
Epoch 272
Validation auc = 0.711737
Epoch 273
Validation auc = 0.707042
Epoch 274
Loss = 1.0092e-03, PNorm = 48.1515, GNorm = 1.4089, lr_0 = 6.3280e-04
Validation auc = 0.704225
Epoch 275
Validation auc = 0.698122
Epoch 276
Validation auc = 0.691080
Epoch 277
Validation auc = 0.695305
Epoch 278
Validation auc = 0.695305
Epoch 279
Loss = 5.0061e-04, PNorm = 48.1938, GNorm = 0.3891, lr_0 = 6.2739e-04
Validation auc = 0.693897
Epoch 280
Validation auc = 0.693427
Epoch 281
Validation auc = 0.693427
Epoch 282
Validation auc = 0.693897
Epoch 283
Validation auc = 0.690610
Epoch 284
Loss = 1.3629e-03, PNorm = 48.2403, GNorm = 0.9418, lr_0 = 6.2203e-04
Validation auc = 0.690610
Epoch 285
Validation auc = 0.690610
Epoch 286
Validation auc = 0.688732
Epoch 287
Validation auc = 0.699531
Epoch 288
Validation auc = 0.702817
Epoch 289
Loss = 4.8196e-04, PNorm = 48.2857, GNorm = 1.1522, lr_0 = 6.1671e-04
Validation auc = 0.705634
Epoch 290
Validation auc = 0.712207
Epoch 291
Validation auc = 0.714085
Epoch 292
Validation auc = 0.715493
Epoch 293
Validation auc = 0.719249
Epoch 294
Loss = 2.7999e-03, PNorm = 48.3297, GNorm = 2.5298, lr_0 = 6.1144e-04
Validation auc = 0.719718
Epoch 295
Validation auc = 0.715023
Epoch 296
Validation auc = 0.709859
Epoch 297
Validation auc = 0.698122
Epoch 298
Validation auc = 0.692019
Epoch 299
Loss = 2.4743e-04, PNorm = 48.3769, GNorm = 0.4836, lr_0 = 6.0621e-04
Validation auc = 0.690141
Model 0 best validation auc = 0.807042 on epoch 6
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.895846
Ensemble test auc = 0.895846
Fold 3
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': 300,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': 1,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_3',
 'save_smiles_splits': False,
 'seed': 3,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': ['sars_cov_two_cl_protease_active'],
 'test': False,
 'test_fold_index': None,
 'train_data_size': 485,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 3
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.753991
Best score so far is 0.753991 at epoch 0 
Epoch 1
Validation auc = 0.778873
Best score so far is 0.778873 at epoch 1 
Epoch 2
Validation auc = 0.791080
Best score so far is 0.791080 at epoch 2 
Epoch 3
Validation auc = 0.797183
Best score so far is 0.797183 at epoch 3 
Epoch 4
Loss = 1.4152e-02, PNorm = 43.6402, GNorm = 3.0971, lr_0 = 6.5000e-04
Validation auc = 0.807512
Best score so far is 0.807512 at epoch 4 
Epoch 5
Validation auc = 0.794836
Epoch 6
Validation auc = 0.790141
Epoch 7
Validation auc = 0.796714
Epoch 8
Validation auc = 0.807042
Epoch 9
Loss = 1.3398e-02, PNorm = 43.7043, GNorm = 2.8660, lr_0 = 9.9743e-04
Validation auc = 0.804225
Epoch 10
Validation auc = 0.765258
Epoch 11
Validation auc = 0.754930
Epoch 12
Validation auc = 0.753052
Epoch 13
Validation auc = 0.763850
Epoch 14
Loss = 1.0162e-02, PNorm = 43.7788, GNorm = 2.6304, lr_0 = 9.8890e-04
Validation auc = 0.787324
Epoch 15
Validation auc = 0.781221
Epoch 16
Validation auc = 0.789671
Epoch 17
Validation auc = 0.784977
Epoch 18
Validation auc = 0.766667
Epoch 19
Loss = 7.5832e-03, PNorm = 43.8427, GNorm = 1.9169, lr_0 = 9.8045e-04
Validation auc = 0.760094
Epoch 20
Validation auc = 0.761033
Epoch 21
Validation auc = 0.772770
Epoch 22
Validation auc = 0.774178
Epoch 23
Validation auc = 0.766667
Epoch 24
Loss = 9.1686e-03, PNorm = 43.8956, GNorm = 2.2250, lr_0 = 9.7207e-04
Validation auc = 0.756338
Epoch 25
Validation auc = 0.746479
Epoch 26
Validation auc = 0.723005
Epoch 27
Validation auc = 0.707042
Epoch 28
Validation auc = 0.694836
Epoch 29
Loss = 8.6893e-03, PNorm = 43.9467, GNorm = 2.8306, lr_0 = 9.6376e-04
Validation auc = 0.703756
Epoch 30
Validation auc = 0.715023
Epoch 31
Validation auc = 0.726291
Epoch 32
Validation auc = 0.726761
Epoch 33
Validation auc = 0.728638
Epoch 34
Loss = 7.4507e-03, PNorm = 43.9964, GNorm = 2.0562, lr_0 = 9.5552e-04
Validation auc = 0.731925
Epoch 35
Validation auc = 0.732864
Epoch 36
Validation auc = 0.727230
Epoch 37
Validation auc = 0.727230
Epoch 38
Validation auc = 0.723005
Epoch 39
Loss = 6.4734e-03, PNorm = 44.0535, GNorm = 2.3098, lr_0 = 9.4735e-04
Validation auc = 0.731455
Epoch 40
Validation auc = 0.733803
Epoch 41
Validation auc = 0.730516
Epoch 42
Validation auc = 0.720657
Epoch 43
Validation auc = 0.713615
Epoch 44
Loss = 8.3250e-03, PNorm = 44.1113, GNorm = 4.1301, lr_0 = 9.3925e-04
Validation auc = 0.709859
Epoch 45
Validation auc = 0.709859
Epoch 46
Validation auc = 0.712676
Epoch 47
Validation auc = 0.721596
Epoch 48
Validation auc = 0.721596
Epoch 49
Loss = 8.0983e-03, PNorm = 44.1770, GNorm = 1.9980, lr_0 = 9.3122e-04
Validation auc = 0.713146
Epoch 50
Validation auc = 0.695305
Epoch 51
Validation auc = 0.691549
Epoch 52
Validation auc = 0.692019
Epoch 53
Validation auc = 0.687793
Epoch 54
Loss = 5.8516e-03, PNorm = 44.2476, GNorm = 2.0291, lr_0 = 9.2326e-04
Validation auc = 0.680751
Epoch 55
Validation auc = 0.672770
Epoch 56
Validation auc = 0.666197
Epoch 57
Validation auc = 0.669014
Epoch 58
Validation auc = 0.677934
Epoch 59
Loss = 7.1227e-03, PNorm = 44.3238, GNorm = 2.1752, lr_0 = 9.1537e-04
Validation auc = 0.686385
Epoch 60
Validation auc = 0.699061
Epoch 61
Validation auc = 0.712676
Epoch 62
Validation auc = 0.717840
Epoch 63
Validation auc = 0.716432
Epoch 64
Loss = 4.6277e-03, PNorm = 44.4120, GNorm = 1.4147, lr_0 = 9.0754e-04
Validation auc = 0.708920
Epoch 65
Validation auc = 0.710329
Epoch 66
Validation auc = 0.712676
Epoch 67
Validation auc = 0.709859
Epoch 68
Validation auc = 0.710798
Epoch 69
Loss = 7.6617e-03, PNorm = 44.5037, GNorm = 2.7948, lr_0 = 8.9978e-04
Validation auc = 0.703756
Epoch 70
Validation auc = 0.710329
Epoch 71
Validation auc = 0.720188
Epoch 72
Validation auc = 0.715962
Epoch 73
Validation auc = 0.719718
Epoch 74
Loss = 4.9240e-03, PNorm = 44.6081, GNorm = 2.4486, lr_0 = 8.9209e-04
Validation auc = 0.726291
Epoch 75
Validation auc = 0.731455
Epoch 76
Validation auc = 0.733803
Epoch 77
Validation auc = 0.731455
Epoch 78
Validation auc = 0.726291
Epoch 79
Loss = 4.9001e-03, PNorm = 44.7027, GNorm = 1.6547, lr_0 = 8.8447e-04
Validation auc = 0.726761
Epoch 80
Validation auc = 0.733333
Epoch 81
Validation auc = 0.738028
Epoch 82
Validation auc = 0.737559
Epoch 83
Validation auc = 0.735211
Epoch 84
Loss = 4.1503e-03, PNorm = 44.7897, GNorm = 2.1193, lr_0 = 8.7691e-04
Validation auc = 0.730986
Epoch 85
Validation auc = 0.722066
Epoch 86
Validation auc = 0.731455
Epoch 87
Validation auc = 0.728638
Epoch 88
Validation auc = 0.722066
Epoch 89
Loss = 6.1040e-03, PNorm = 44.8859, GNorm = 1.9494, lr_0 = 8.6941e-04
Validation auc = 0.710329
Epoch 90
Validation auc = 0.707042
Epoch 91
Validation auc = 0.704695
Epoch 92
Validation auc = 0.706103
Epoch 93
Validation auc = 0.712676
Epoch 94
Loss = 3.7837e-03, PNorm = 44.9815, GNorm = 1.4641, lr_0 = 8.6198e-04
Validation auc = 0.718310
Epoch 95
Validation auc = 0.730047
Epoch 96
Validation auc = 0.734742
Epoch 97
Validation auc = 0.741315
Epoch 98
Validation auc = 0.737559
Epoch 99
Loss = 4.6079e-03, PNorm = 45.0659, GNorm = 1.7138, lr_0 = 8.5461e-04
Validation auc = 0.738028
Epoch 100
Validation auc = 0.741784
Epoch 101
Validation auc = 0.750235
Epoch 102
Validation auc = 0.751643
Epoch 103
Validation auc = 0.742254
Epoch 104
Loss = 4.6522e-03, PNorm = 45.1805, GNorm = 2.1254, lr_0 = 8.4730e-04
Validation auc = 0.734272
Epoch 105
Validation auc = 0.729577
Epoch 106
Validation auc = 0.738967
Epoch 107
Validation auc = 0.736620
Epoch 108
Validation auc = 0.741784
Epoch 109
Loss = 2.8504e-03, PNorm = 45.2947, GNorm = 0.7188, lr_0 = 8.4006e-04
Validation auc = 0.743662
Epoch 110
Validation auc = 0.744601
Epoch 111
Validation auc = 0.744131
Epoch 112
Validation auc = 0.749296
Epoch 113
Validation auc = 0.757277
Epoch 114
Loss = 3.9296e-03, PNorm = 45.4004, GNorm = 1.2381, lr_0 = 8.3288e-04
Validation auc = 0.754930
Epoch 115
Validation auc = 0.753052
Epoch 116
Validation auc = 0.753521
Epoch 117
Validation auc = 0.752582
Epoch 118
Validation auc = 0.742254
Epoch 119
Loss = 3.3239e-03, PNorm = 45.5255, GNorm = 1.1592, lr_0 = 8.2576e-04
Validation auc = 0.739906
Epoch 120
Validation auc = 0.746479
Epoch 121
Validation auc = 0.744131
Epoch 122
Validation auc = 0.744601
Epoch 123
Validation auc = 0.749296
Epoch 124
Loss = 4.8404e-03, PNorm = 45.6395, GNorm = 1.9861, lr_0 = 8.1870e-04
Validation auc = 0.742254
Epoch 125
Validation auc = 0.742723
Epoch 126
Validation auc = 0.737089
Epoch 127
Validation auc = 0.741784
Epoch 128
Validation auc = 0.737089
Epoch 129
Loss = 2.8466e-03, PNorm = 45.7720, GNorm = 1.5201, lr_0 = 8.1170e-04
Validation auc = 0.739437
Epoch 130
Validation auc = 0.729108
Epoch 131
Validation auc = 0.744131
Epoch 132
Validation auc = 0.752582
Epoch 133
Validation auc = 0.750235
Epoch 134
Loss = 4.7426e-03, PNorm = 45.8942, GNorm = 2.1129, lr_0 = 8.0476e-04
Validation auc = 0.737559
Epoch 135
Validation auc = 0.727230
Epoch 136
Validation auc = 0.715493
Epoch 137
Validation auc = 0.703286
Epoch 138
Validation auc = 0.723944
Epoch 139
Loss = 2.1720e-03, PNorm = 46.0078, GNorm = 1.9518, lr_0 = 7.9788e-04
Validation auc = 0.729108
Epoch 140
Validation auc = 0.735211
Epoch 141
Validation auc = 0.728169
Epoch 142
Validation auc = 0.721127
Epoch 143
Validation auc = 0.707042
Epoch 144
Loss = 3.8675e-03, PNorm = 46.1295, GNorm = 4.0147, lr_0 = 7.9106e-04
Validation auc = 0.711737
Epoch 145
Validation auc = 0.720188
Epoch 146
Validation auc = 0.714085
Epoch 147
Validation auc = 0.710329
Epoch 148
Validation auc = 0.722535
Epoch 149
Loss = 2.5024e-03, PNorm = 46.2394, GNorm = 1.9266, lr_0 = 7.8430e-04
Validation auc = 0.727700
Epoch 150
Validation auc = 0.727230
Epoch 151
Validation auc = 0.723944
Epoch 152
Validation auc = 0.729577
Epoch 153
Validation auc = 0.738967
Epoch 154
Loss = 2.4193e-03, PNorm = 46.3536, GNorm = 1.8016, lr_0 = 7.7759e-04
Validation auc = 0.745070
Epoch 155
Validation auc = 0.752113
Epoch 156
Validation auc = 0.751174
Epoch 157
Validation auc = 0.743662
Epoch 158
Validation auc = 0.740376
Epoch 159
Loss = 3.7515e-03, PNorm = 46.4742, GNorm = 1.3931, lr_0 = 7.7095e-04
Validation auc = 0.742254
Epoch 160
Validation auc = 0.739437
Epoch 161
Validation auc = 0.734742
Epoch 162
Validation auc = 0.731455
Epoch 163
Validation auc = 0.728169
Epoch 164
Loss = 3.0670e-03, PNorm = 46.5847, GNorm = 1.0289, lr_0 = 7.6436e-04
Validation auc = 0.727700
Epoch 165
Validation auc = 0.730986
Epoch 166
Validation auc = 0.732394
Epoch 167
Validation auc = 0.728638
Epoch 168
Validation auc = 0.722535
Epoch 169
Loss = 1.4803e-03, PNorm = 46.6808, GNorm = 2.0108, lr_0 = 7.5782e-04
Validation auc = 0.721596
Epoch 170
Validation auc = 0.721596
Epoch 171
Validation auc = 0.722535
Epoch 172
Validation auc = 0.716901
Epoch 173
Validation auc = 0.699531
Epoch 174
Loss = 4.2008e-03, PNorm = 46.7650, GNorm = 3.8874, lr_0 = 7.5134e-04
Validation auc = 0.710798
Epoch 175
Validation auc = 0.718779
Epoch 176
Validation auc = 0.725822
Epoch 177
Validation auc = 0.723474
Epoch 178
Validation auc = 0.720657
Epoch 179
Loss = 2.1320e-03, PNorm = 46.8500, GNorm = 1.2817, lr_0 = 7.4492e-04
Validation auc = 0.719718
Epoch 180
Validation auc = 0.719249
Epoch 181
Validation auc = 0.717371
Epoch 182
Validation auc = 0.722535
Epoch 183
Validation auc = 0.721596
Epoch 184
Loss = 9.9208e-04, PNorm = 46.9449, GNorm = 0.8003, lr_0 = 7.3855e-04
Validation auc = 0.718779
Epoch 185
Validation auc = 0.714085
Epoch 186
Validation auc = 0.721596
Epoch 187
Validation auc = 0.720657
Epoch 188
Validation auc = 0.712676
Epoch 189
Loss = 1.1405e-03, PNorm = 47.0355, GNorm = 0.5305, lr_0 = 7.3224e-04
Validation auc = 0.704695
Epoch 190
Validation auc = 0.697183
Epoch 191
Validation auc = 0.693427
Epoch 192
Validation auc = 0.698122
Epoch 193
Validation auc = 0.700939
Epoch 194
Loss = 2.5366e-03, PNorm = 47.1185, GNorm = 0.7891, lr_0 = 7.2598e-04
Validation auc = 0.687793
Epoch 195
Validation auc = 0.684977
Epoch 196
Validation auc = 0.697653
Epoch 197
Validation auc = 0.713146
Epoch 198
Validation auc = 0.716901
Epoch 199
Loss = 1.1574e-03, PNorm = 47.2165, GNorm = 0.7127, lr_0 = 7.1977e-04
Validation auc = 0.713146
Epoch 200
Validation auc = 0.712676
Epoch 201
Validation auc = 0.712676
Epoch 202
Validation auc = 0.712207
Epoch 203
Validation auc = 0.718310
Epoch 204
Loss = 8.0401e-04, PNorm = 47.3091, GNorm = 0.6817, lr_0 = 7.1362e-04
Validation auc = 0.723944
Epoch 205
Validation auc = 0.726291
Epoch 206
Validation auc = 0.724413
Epoch 207
Validation auc = 0.721127
Epoch 208
Validation auc = 0.720657
Epoch 209
Loss = 1.7406e-03, PNorm = 47.3850, GNorm = 0.5333, lr_0 = 7.0752e-04
Validation auc = 0.725352
Epoch 210
Validation auc = 0.717840
Epoch 211
Validation auc = 0.707512
Epoch 212
Validation auc = 0.692958
Epoch 213
Validation auc = 0.685446
Epoch 214
Loss = 1.5545e-03, PNorm = 47.4419, GNorm = 0.8067, lr_0 = 7.0147e-04
Validation auc = 0.684977
Epoch 215
Validation auc = 0.689671
Epoch 216
Validation auc = 0.688732
Epoch 217
Validation auc = 0.684507
Epoch 218
Validation auc = 0.685915
Epoch 219
Loss = 9.7992e-04, PNorm = 47.5086, GNorm = 1.6032, lr_0 = 6.9548e-04
Validation auc = 0.692958
Epoch 220
Validation auc = 0.700469
Epoch 221
Validation auc = 0.704225
Epoch 222
Validation auc = 0.701878
Epoch 223
Validation auc = 0.694366
Epoch 224
Loss = 5.0627e-04, PNorm = 47.5831, GNorm = 0.2397, lr_0 = 6.8953e-04
Validation auc = 0.692488
Epoch 225
Validation auc = 0.694366
Epoch 226
Validation auc = 0.700000
Epoch 227
Validation auc = 0.697183
Epoch 228
Validation auc = 0.702817
Epoch 229
Loss = 1.8998e-03, PNorm = 47.6415, GNorm = 1.2132, lr_0 = 6.8364e-04
Validation auc = 0.701878
Epoch 230
Validation auc = 0.701878
Epoch 231
Validation auc = 0.694366
Epoch 232
Validation auc = 0.688263
Epoch 233
Validation auc = 0.685446
Epoch 234
Loss = 1.2645e-03, PNorm = 47.7088, GNorm = 0.9201, lr_0 = 6.7779e-04
Validation auc = 0.692488
Epoch 235
Validation auc = 0.695775
Epoch 236
Validation auc = 0.693897
Epoch 237
Validation auc = 0.690141
Epoch 238
Validation auc = 0.692958
Epoch 239
Loss = 4.3528e-04, PNorm = 47.7647, GNorm = 0.9156, lr_0 = 6.7200e-04
Validation auc = 0.693427
Epoch 240
Validation auc = 0.698122
Epoch 241
Validation auc = 0.699061
Epoch 242
Validation auc = 0.689202
Epoch 243
Validation auc = 0.683568
Epoch 244
Loss = 3.1176e-03, PNorm = 47.8136, GNorm = 2.5215, lr_0 = 6.6625e-04
Validation auc = 0.691080
Epoch 245
Validation auc = 0.700469
Epoch 246
Validation auc = 0.710798
Epoch 247
Validation auc = 0.711737
Epoch 248
Validation auc = 0.703286
Epoch 249
Loss = 2.5458e-04, PNorm = 47.8780, GNorm = 0.3536, lr_0 = 6.6056e-04
Validation auc = 0.701408
Epoch 250
Validation auc = 0.700469
Epoch 251
Validation auc = 0.705634
Epoch 252
Validation auc = 0.703286
Epoch 253
Validation auc = 0.701878
Epoch 254
Loss = 6.2278e-04, PNorm = 47.9511, GNorm = 1.0518, lr_0 = 6.5491e-04
Validation auc = 0.700939
Epoch 255
Validation auc = 0.698122
Epoch 256
Validation auc = 0.702817
Epoch 257
Validation auc = 0.703756
Epoch 258
Validation auc = 0.712676
Epoch 259
Loss = 9.1024e-04, PNorm = 48.0016, GNorm = 1.5166, lr_0 = 6.4931e-04
Validation auc = 0.713615
Epoch 260
Validation auc = 0.712207
Epoch 261
Validation auc = 0.706573
Epoch 262
Validation auc = 0.696244
Epoch 263
Validation auc = 0.697183
Epoch 264
Loss = 6.0070e-04, PNorm = 48.0738, GNorm = 0.3196, lr_0 = 6.4376e-04
Validation auc = 0.701408
Epoch 265
Validation auc = 0.702817
Epoch 266
Validation auc = 0.700000
Epoch 267
Validation auc = 0.698122
Epoch 268
Validation auc = 0.694366
Epoch 269
Loss = 4.9116e-04, PNorm = 48.1363, GNorm = 0.5250, lr_0 = 6.3826e-04
Validation auc = 0.692958
Epoch 270
Validation auc = 0.687793
Epoch 271
Validation auc = 0.685915
Epoch 272
Validation auc = 0.682629
Epoch 273
Validation auc = 0.684507
Epoch 274
Loss = 3.1841e-04, PNorm = 48.1913, GNorm = 0.6401, lr_0 = 6.3280e-04
Validation auc = 0.689671
Epoch 275
Validation auc = 0.686385
Epoch 276
Validation auc = 0.688732
Epoch 277
Validation auc = 0.686385
Epoch 278
Validation auc = 0.684507
Epoch 279
Loss = 2.4201e-04, PNorm = 48.2391, GNorm = 0.5560, lr_0 = 6.2739e-04
Validation auc = 0.684038
Epoch 280
Validation auc = 0.690141
Epoch 281
Validation auc = 0.693897
Epoch 282
Validation auc = 0.688732
Epoch 283
Validation auc = 0.678404
Epoch 284
Loss = 1.3565e-03, PNorm = 48.2837, GNorm = 0.0952, lr_0 = 6.2203e-04
Validation auc = 0.674648
Epoch 285
Validation auc = 0.682629
Epoch 286
Validation auc = 0.686854
Epoch 287
Validation auc = 0.692958
Epoch 288
Validation auc = 0.694836
Epoch 289
Loss = 4.8913e-04, PNorm = 48.3266, GNorm = 1.0824, lr_0 = 6.1671e-04
Validation auc = 0.695775
Epoch 290
Validation auc = 0.699061
Epoch 291
Validation auc = 0.705634
Epoch 292
Validation auc = 0.706103
Epoch 293
Validation auc = 0.701878
Epoch 294
Loss = 4.4329e-04, PNorm = 48.3746, GNorm = 0.1814, lr_0 = 6.1144e-04
Validation auc = 0.694836
Epoch 295
Validation auc = 0.696244
Epoch 296
Validation auc = 0.703286
Epoch 297
Validation auc = 0.707512
Epoch 298
Validation auc = 0.707981
Epoch 299
Loss = 7.2458e-04, PNorm = 48.4175, GNorm = 0.6316, lr_0 = 6.0621e-04
Validation auc = 0.704695
Model 0 best validation auc = 0.807512 on epoch 4
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.860927
Ensemble test auc = 0.860927
Fold 4
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': 300,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': 1,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_4',
 'save_smiles_splits': False,
 'seed': 4,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': ['sars_cov_two_cl_protease_active'],
 'test': False,
 'test_fold_index': None,
 'train_data_size': 485,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 4
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.747418
Best score so far is 0.747418 at epoch 0 
Epoch 1
Validation auc = 0.762911
Best score so far is 0.762911 at epoch 1 
Epoch 2
Validation auc = 0.761972
Epoch 3
Validation auc = 0.760563
Epoch 4
Loss = 1.8653e-02, PNorm = 43.6383, GNorm = 4.5822, lr_0 = 6.5000e-04
Validation auc = 0.757277
Epoch 5
Validation auc = 0.769484
Best score so far is 0.769484 at epoch 5 
Epoch 6
Validation auc = 0.781690
Best score so far is 0.781690 at epoch 6 
Epoch 7
Validation auc = 0.798592
Best score so far is 0.798592 at epoch 7 
Epoch 8
Validation auc = 0.805634
Best score so far is 0.805634 at epoch 8 
Epoch 9
Loss = 1.0414e-02, PNorm = 43.6933, GNorm = 2.6187, lr_0 = 9.9743e-04
Validation auc = 0.800469
Epoch 10
Validation auc = 0.793427
Epoch 11
Validation auc = 0.772300
Epoch 12
Validation auc = 0.765258
Epoch 13
Validation auc = 0.768075
Epoch 14
Loss = 1.0206e-02, PNorm = 43.7634, GNorm = 2.9150, lr_0 = 9.8890e-04
Validation auc = 0.761502
Epoch 15
Validation auc = 0.770892
Epoch 16
Validation auc = 0.780282
Epoch 17
Validation auc = 0.786854
Epoch 18
Validation auc = 0.800939
Epoch 19
Loss = 9.9693e-03, PNorm = 43.8245, GNorm = 2.6176, lr_0 = 9.8045e-04
Validation auc = 0.790610
Epoch 20
Validation auc = 0.773239
Epoch 21
Validation auc = 0.749296
Epoch 22
Validation auc = 0.736150
Epoch 23
Validation auc = 0.739437
Epoch 24
Loss = 8.3989e-03, PNorm = 43.8779, GNorm = 1.9243, lr_0 = 9.7207e-04
Validation auc = 0.739906
Epoch 25
Validation auc = 0.747418
Epoch 26
Validation auc = 0.738967
Epoch 27
Validation auc = 0.743192
Epoch 28
Validation auc = 0.743192
Epoch 29
Loss = 9.0712e-03, PNorm = 43.9312, GNorm = 3.8735, lr_0 = 9.6376e-04
Validation auc = 0.734272
Epoch 30
Validation auc = 0.718779
Epoch 31
Validation auc = 0.705634
Epoch 32
Validation auc = 0.707981
Epoch 33
Validation auc = 0.700939
Epoch 34
Loss = 7.8530e-03, PNorm = 43.9878, GNorm = 2.6587, lr_0 = 9.5552e-04
Validation auc = 0.714085
Epoch 35
Validation auc = 0.720188
Epoch 36
Validation auc = 0.718310
Epoch 37
Validation auc = 0.703286
Epoch 38
Validation auc = 0.709390
Epoch 39
Loss = 6.9853e-03, PNorm = 44.0497, GNorm = 1.7125, lr_0 = 9.4735e-04
Validation auc = 0.713146
Epoch 40
Validation auc = 0.713615
Epoch 41
Validation auc = 0.716432
Epoch 42
Validation auc = 0.725822
Epoch 43
Validation auc = 0.722535
Epoch 44
Loss = 6.8035e-03, PNorm = 44.1222, GNorm = 3.6865, lr_0 = 9.3925e-04
Validation auc = 0.707981
Epoch 45
Validation auc = 0.701408
Epoch 46
Validation auc = 0.695305
Epoch 47
Validation auc = 0.692488
Epoch 48
Validation auc = 0.680751
Epoch 49
Loss = 6.2661e-03, PNorm = 44.2036, GNorm = 2.2712, lr_0 = 9.3122e-04
Validation auc = 0.683568
Epoch 50
Validation auc = 0.691080
Epoch 51
Validation auc = 0.704225
Epoch 52
Validation auc = 0.703286
Epoch 53
Validation auc = 0.701408
Epoch 54
Loss = 6.5994e-03, PNorm = 44.2913, GNorm = 1.7844, lr_0 = 9.2326e-04
Validation auc = 0.702817
Epoch 55
Validation auc = 0.705634
Epoch 56
Validation auc = 0.705164
Epoch 57
Validation auc = 0.703286
Epoch 58
Validation auc = 0.707042
Epoch 59
Loss = 1.0771e-02, PNorm = 44.3689, GNorm = 4.2578, lr_0 = 9.1537e-04
Validation auc = 0.705164
Epoch 60
Validation auc = 0.704695
Epoch 61
Validation auc = 0.708451
Epoch 62
Validation auc = 0.711737
Epoch 63
Validation auc = 0.715023
Epoch 64
Loss = 6.0970e-03, PNorm = 44.4627, GNorm = 2.3760, lr_0 = 9.0754e-04
Validation auc = 0.717371
Epoch 65
Validation auc = 0.711268
Epoch 66
Validation auc = 0.714085
Epoch 67
Validation auc = 0.723474
Epoch 68
Validation auc = 0.725352
Epoch 69
Loss = 5.8274e-03, PNorm = 44.5571, GNorm = 2.0383, lr_0 = 8.9978e-04
Validation auc = 0.723005
Epoch 70
Validation auc = 0.713146
Epoch 71
Validation auc = 0.705634
Epoch 72
Validation auc = 0.691080
Epoch 73
Validation auc = 0.692019
Epoch 74
Loss = 5.6945e-03, PNorm = 44.6576, GNorm = 2.0405, lr_0 = 8.9209e-04
Validation auc = 0.692958
Epoch 75
Validation auc = 0.703756
Epoch 76
Validation auc = 0.715962
Epoch 77
Validation auc = 0.725352
Epoch 78
Validation auc = 0.736150
Epoch 79
Loss = 6.7765e-03, PNorm = 44.7517, GNorm = 2.2722, lr_0 = 8.8447e-04
Validation auc = 0.740376
Epoch 80
Validation auc = 0.741315
Epoch 81
Validation auc = 0.732394
Epoch 82
Validation auc = 0.725352
Epoch 83
Validation auc = 0.722535
Epoch 84
Loss = 5.3888e-03, PNorm = 44.8360, GNorm = 2.9028, lr_0 = 8.7691e-04
Validation auc = 0.721127
Epoch 85
Validation auc = 0.723944
Epoch 86
Validation auc = 0.730986
Epoch 87
Validation auc = 0.727230
Epoch 88
Validation auc = 0.730516
Epoch 89
Loss = 4.1905e-03, PNorm = 44.9280, GNorm = 2.0047, lr_0 = 8.6941e-04
Validation auc = 0.730986
Epoch 90
Validation auc = 0.730516
Epoch 91
Validation auc = 0.730516
Epoch 92
Validation auc = 0.733333
Epoch 93
Validation auc = 0.741784
Epoch 94
Loss = 5.6729e-03, PNorm = 45.0254, GNorm = 2.2275, lr_0 = 8.6198e-04
Validation auc = 0.733803
Epoch 95
Validation auc = 0.722066
Epoch 96
Validation auc = 0.730047
Epoch 97
Validation auc = 0.735681
Epoch 98
Validation auc = 0.738967
Epoch 99
Loss = 3.2790e-03, PNorm = 45.1380, GNorm = 1.4947, lr_0 = 8.5461e-04
Validation auc = 0.743192
Epoch 100
Validation auc = 0.745540
Epoch 101
Validation auc = 0.747418
Epoch 102
Validation auc = 0.755399
Epoch 103
Validation auc = 0.759155
Epoch 104
Loss = 2.3128e-03, PNorm = 45.2431, GNorm = 1.3106, lr_0 = 8.4730e-04
Validation auc = 0.755869
Epoch 105
Validation auc = 0.754460
Epoch 106
Validation auc = 0.738028
Epoch 107
Validation auc = 0.736150
Epoch 108
Validation auc = 0.746479
Epoch 109
Loss = 6.1974e-03, PNorm = 45.3560, GNorm = 2.4129, lr_0 = 8.4006e-04
Validation auc = 0.747418
Epoch 110
Validation auc = 0.745540
Epoch 111
Validation auc = 0.750235
Epoch 112
Validation auc = 0.751174
Epoch 113
Validation auc = 0.753521
Epoch 114
Loss = 3.4054e-03, PNorm = 45.4722, GNorm = 1.4774, lr_0 = 8.3288e-04
Validation auc = 0.751174
Epoch 115
Validation auc = 0.751174
Epoch 116
Validation auc = 0.759155
Epoch 117
Validation auc = 0.761972
Epoch 118
Validation auc = 0.761033
Epoch 119
Loss = 4.9317e-03, PNorm = 45.5849, GNorm = 2.3773, lr_0 = 8.2576e-04
Validation auc = 0.755869
Epoch 120
Validation auc = 0.747418
Epoch 121
Validation auc = 0.743192
Epoch 122
Validation auc = 0.746009
Epoch 123
Validation auc = 0.744601
Epoch 124
Loss = 2.5704e-03, PNorm = 45.7025, GNorm = 0.7223, lr_0 = 8.1870e-04
Validation auc = 0.736150
Epoch 125
Validation auc = 0.732864
Epoch 126
Validation auc = 0.737089
Epoch 127
Validation auc = 0.741315
Epoch 128
Validation auc = 0.738028
Epoch 129
Loss = 2.5323e-03, PNorm = 45.8181, GNorm = 1.2010, lr_0 = 8.1170e-04
Validation auc = 0.742254
Epoch 130
Validation auc = 0.747418
Epoch 131
Validation auc = 0.741315
Epoch 132
Validation auc = 0.741315
Epoch 133
Validation auc = 0.742723
Epoch 134
Loss = 4.3782e-03, PNorm = 45.9255, GNorm = 2.0165, lr_0 = 8.0476e-04
Validation auc = 0.738498
Epoch 135
Validation auc = 0.740845
Epoch 136
Validation auc = 0.736150
Epoch 137
Validation auc = 0.737089
Epoch 138
Validation auc = 0.743662
Epoch 139
Loss = 2.8793e-03, PNorm = 46.0384, GNorm = 1.1886, lr_0 = 7.9788e-04
Validation auc = 0.747418
Epoch 140
Validation auc = 0.750235
Epoch 141
Validation auc = 0.746009
Epoch 142
Validation auc = 0.750704
Epoch 143
Validation auc = 0.752582
Epoch 144
Loss = 2.8001e-03, PNorm = 46.1426, GNorm = 1.1447, lr_0 = 7.9106e-04
Validation auc = 0.758216
Epoch 145
Validation auc = 0.750704
Epoch 146
Validation auc = 0.745070
Epoch 147
Validation auc = 0.748826
Epoch 148
Validation auc = 0.747418
Epoch 149
Loss = 3.1348e-03, PNorm = 46.2413, GNorm = 2.0049, lr_0 = 7.8430e-04
Validation auc = 0.738967
Epoch 150
Validation auc = 0.725352
Epoch 151
Validation auc = 0.707042
Epoch 152
Validation auc = 0.698592
Epoch 153
Validation auc = 0.704695
Epoch 154
Loss = 4.3568e-03, PNorm = 46.3447, GNorm = 2.3630, lr_0 = 7.7759e-04
Validation auc = 0.723005
Epoch 155
Validation auc = 0.727230
Epoch 156
Validation auc = 0.738967
Epoch 157
Validation auc = 0.739906
Epoch 158
Validation auc = 0.743192
Epoch 159
Loss = 3.6516e-03, PNorm = 46.4477, GNorm = 1.1713, lr_0 = 7.7095e-04
Validation auc = 0.740845
Epoch 160
Validation auc = 0.740376
Epoch 161
Validation auc = 0.746948
Epoch 162
Validation auc = 0.746948
Epoch 163
Validation auc = 0.730516
Epoch 164
Loss = 4.0895e-03, PNorm = 46.5840, GNorm = 2.8620, lr_0 = 7.6436e-04
Validation auc = 0.734742
Epoch 165
Validation auc = 0.741784
Epoch 166
Validation auc = 0.742723
Epoch 167
Validation auc = 0.747887
Epoch 168
Validation auc = 0.747418
Epoch 169
Loss = 2.0167e-03, PNorm = 46.7034, GNorm = 1.3075, lr_0 = 7.5782e-04
Validation auc = 0.746009
Epoch 170
Validation auc = 0.745540
Epoch 171
Validation auc = 0.748357
Epoch 172
Validation auc = 0.745070
Epoch 173
Validation auc = 0.739906
Epoch 174
Loss = 1.4990e-03, PNorm = 46.7973, GNorm = 1.3451, lr_0 = 7.5134e-04
Validation auc = 0.731925
Epoch 175
Validation auc = 0.727230
Epoch 176
Validation auc = 0.725822
Epoch 177
Validation auc = 0.728169
Epoch 178
Validation auc = 0.721127
Epoch 179
Loss = 1.8220e-03, PNorm = 46.8982, GNorm = 1.5263, lr_0 = 7.4492e-04
Validation auc = 0.716901
Epoch 180
Validation auc = 0.719249
Epoch 181
Validation auc = 0.721596
Epoch 182
Validation auc = 0.707512
Epoch 183
Validation auc = 0.698592
Epoch 184
Loss = 3.4639e-03, PNorm = 46.9891, GNorm = 1.1320, lr_0 = 7.3855e-04
Validation auc = 0.707042
Epoch 185
Validation auc = 0.707042
Epoch 186
Validation auc = 0.707042
Epoch 187
Validation auc = 0.707512
Epoch 188
Validation auc = 0.712676
Epoch 189
Loss = 1.5727e-03, PNorm = 47.0776, GNorm = 0.6313, lr_0 = 7.3224e-04
Validation auc = 0.714085
Epoch 190
Validation auc = 0.716432
Epoch 191
Validation auc = 0.719718
Epoch 192
Validation auc = 0.723944
Epoch 193
Validation auc = 0.723005
Epoch 194
Loss = 2.4607e-03, PNorm = 47.1682, GNorm = 1.3498, lr_0 = 7.2598e-04
Validation auc = 0.718779
Epoch 195
Validation auc = 0.722535
Epoch 196
Validation auc = 0.713615
Epoch 197
Validation auc = 0.709859
Epoch 198
Validation auc = 0.703286
Epoch 199
Loss = 9.7473e-04, PNorm = 47.2570, GNorm = 0.8086, lr_0 = 7.1977e-04
Validation auc = 0.689202
Epoch 200
Validation auc = 0.682629
Epoch 201
Validation auc = 0.692958
Epoch 202
Validation auc = 0.709859
Epoch 203
Validation auc = 0.699061
Epoch 204
Loss = 5.7226e-04, PNorm = 47.3478, GNorm = 0.4914, lr_0 = 7.1362e-04
Validation auc = 0.681690
Epoch 205
Validation auc = 0.686854
Epoch 206
Validation auc = 0.698592
Epoch 207
Validation auc = 0.714085
Epoch 208
Validation auc = 0.719718
Epoch 209
Loss = 1.8163e-03, PNorm = 47.4415, GNorm = 1.0323, lr_0 = 7.0752e-04
Validation auc = 0.715962
Epoch 210
Validation auc = 0.705634
Epoch 211
Validation auc = 0.704695
Epoch 212
Validation auc = 0.702817
Epoch 213
Validation auc = 0.703756
Epoch 214
Loss = 2.6458e-03, PNorm = 47.5462, GNorm = 2.2560, lr_0 = 7.0147e-04
Validation auc = 0.699061
Epoch 215
Validation auc = 0.696714
Epoch 216
Validation auc = 0.694366
Epoch 217
Validation auc = 0.696714
Epoch 218
Validation auc = 0.703286
Epoch 219
Loss = 1.0467e-03, PNorm = 47.6285, GNorm = 1.0479, lr_0 = 6.9548e-04
Validation auc = 0.711737
Epoch 220
Validation auc = 0.716432
Epoch 221
Validation auc = 0.713615
Epoch 222
Validation auc = 0.712676
Epoch 223
Validation auc = 0.712207
Epoch 224
Loss = 8.9206e-04, PNorm = 47.7093, GNorm = 0.9793, lr_0 = 6.8953e-04
Validation auc = 0.714085
Epoch 225
Validation auc = 0.713615
Epoch 226
Validation auc = 0.711268
Epoch 227
Validation auc = 0.702347
Epoch 228
Validation auc = 0.706103
Epoch 229
Loss = 7.7917e-04, PNorm = 47.7738, GNorm = 0.5554, lr_0 = 6.8364e-04
Validation auc = 0.707512
Epoch 230
Validation auc = 0.710798
Epoch 231
Validation auc = 0.706573
Epoch 232
Validation auc = 0.702347
Epoch 233
Validation auc = 0.701878
Epoch 234
Loss = 6.6754e-04, PNorm = 47.8449, GNorm = 0.5720, lr_0 = 6.7779e-04
Validation auc = 0.696714
Epoch 235
Validation auc = 0.697653
Epoch 236
Validation auc = 0.696244
Epoch 237
Validation auc = 0.695775
Epoch 238
Validation auc = 0.698592
Epoch 239
Loss = 3.7847e-04, PNorm = 47.9084, GNorm = 0.3176, lr_0 = 6.7200e-04
Validation auc = 0.704695
Epoch 240
Validation auc = 0.714085
Epoch 241
Validation auc = 0.719249
Epoch 242
Validation auc = 0.720657
Epoch 243
Validation auc = 0.715493
Epoch 244
Loss = 7.7819e-04, PNorm = 47.9690, GNorm = 0.4539, lr_0 = 6.6625e-04
Validation auc = 0.711737
Epoch 245
Validation auc = 0.709390
Epoch 246
Validation auc = 0.708920
Epoch 247
Validation auc = 0.710329
Epoch 248
Validation auc = 0.709390
Epoch 249
Loss = 1.2439e-03, PNorm = 48.0291, GNorm = 0.3655, lr_0 = 6.6056e-04
Validation auc = 0.704225
Epoch 250
Validation auc = 0.701878
Epoch 251
Validation auc = 0.703756
Epoch 252
Validation auc = 0.710329
Epoch 253
Validation auc = 0.718779
Epoch 254
Loss = 1.1690e-03, PNorm = 48.0735, GNorm = 1.1432, lr_0 = 6.5491e-04
Validation auc = 0.721596
Epoch 255
Validation auc = 0.724413
Epoch 256
Validation auc = 0.723474
Epoch 257
Validation auc = 0.719718
Epoch 258
Validation auc = 0.712676
Epoch 259
Loss = 5.2489e-04, PNorm = 48.1316, GNorm = 0.7485, lr_0 = 6.4931e-04
Validation auc = 0.703286
Epoch 260
Validation auc = 0.700939
Epoch 261
Validation auc = 0.697183
Epoch 262
Validation auc = 0.691549
Epoch 263
Validation auc = 0.690610
Epoch 264
Loss = 6.5094e-04, PNorm = 48.1842, GNorm = 0.3899, lr_0 = 6.4376e-04
Validation auc = 0.689671
Epoch 265
Validation auc = 0.691549
Epoch 266
Validation auc = 0.690610
Epoch 267
Validation auc = 0.690610
Epoch 268
Validation auc = 0.683568
Epoch 269
Loss = 8.2976e-04, PNorm = 48.2292, GNorm = 1.3284, lr_0 = 6.3826e-04
Validation auc = 0.680282
Epoch 270
Validation auc = 0.685446
Epoch 271
Validation auc = 0.684507
Epoch 272
Validation auc = 0.684507
Epoch 273
Validation auc = 0.681221
Epoch 274
Loss = 6.3275e-04, PNorm = 48.2713, GNorm = 1.5757, lr_0 = 6.3280e-04
Validation auc = 0.687324
Epoch 275
Validation auc = 0.708451
Epoch 276
Validation auc = 0.723944
Epoch 277
Validation auc = 0.729577
Epoch 278
Validation auc = 0.722535
Epoch 279
Loss = 1.4014e-03, PNorm = 48.3298, GNorm = 0.8282, lr_0 = 6.2739e-04
Validation auc = 0.722535
Epoch 280
Validation auc = 0.720188
Epoch 281
Validation auc = 0.720657
Epoch 282
Validation auc = 0.720188
Epoch 283
Validation auc = 0.717371
Epoch 284
Loss = 1.1887e-03, PNorm = 48.4181, GNorm = 0.9455, lr_0 = 6.2203e-04
Validation auc = 0.716432
Epoch 285
Validation auc = 0.712676
Epoch 286
Validation auc = 0.706103
Epoch 287
Validation auc = 0.705164
Epoch 288
Validation auc = 0.703286
Epoch 289
Loss = 1.7310e-03, PNorm = 48.5227, GNorm = 1.5945, lr_0 = 6.1671e-04
Validation auc = 0.705164
Epoch 290
Validation auc = 0.707512
Epoch 291
Validation auc = 0.709859
Epoch 292
Validation auc = 0.711268
Epoch 293
Validation auc = 0.706103
Epoch 294
Loss = 2.8938e-04, PNorm = 48.5892, GNorm = 0.1579, lr_0 = 6.1144e-04
Validation auc = 0.704225
Epoch 295
Validation auc = 0.702347
Epoch 296
Validation auc = 0.705634
Epoch 297
Validation auc = 0.710798
Epoch 298
Validation auc = 0.714554
Epoch 299
Loss = 1.1813e-03, PNorm = 48.6338, GNorm = 1.3428, lr_0 = 6.0621e-04
Validation auc = 0.715023
Model 0 best validation auc = 0.805634 on epoch 8
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.911499
Ensemble test auc = 0.911499
Fold 5
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': 300,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': 1,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_5',
 'save_smiles_splits': False,
 'seed': 5,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': ['sars_cov_two_cl_protease_active'],
 'test': False,
 'test_fold_index': None,
 'train_data_size': 485,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 5
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.750235
Best score so far is 0.750235 at epoch 0 
Epoch 1
Validation auc = 0.770423
Best score so far is 0.770423 at epoch 1 
Epoch 2
Validation auc = 0.784038
Best score so far is 0.784038 at epoch 2 
Epoch 3
Validation auc = 0.787793
Best score so far is 0.787793 at epoch 3 
Epoch 4
Loss = 1.2533e-02, PNorm = 43.6372, GNorm = 3.1044, lr_0 = 6.5000e-04
Validation auc = 0.779343
Epoch 5
Validation auc = 0.776056
Epoch 6
Validation auc = 0.793897
Best score so far is 0.793897 at epoch 6 
Epoch 7
Validation auc = 0.796714
Best score so far is 0.796714 at epoch 7 
Epoch 8
Validation auc = 0.810329
Best score so far is 0.810329 at epoch 8 
Epoch 9
Loss = 1.2003e-02, PNorm = 43.6937, GNorm = 3.1873, lr_0 = 9.9743e-04
Validation auc = 0.794836
Epoch 10
Validation auc = 0.788732
Epoch 11
Validation auc = 0.758216
Epoch 12
Validation auc = 0.737089
Epoch 13
Validation auc = 0.736150
Epoch 14
Loss = 9.4901e-03, PNorm = 43.7682, GNorm = 3.3729, lr_0 = 9.8890e-04
Validation auc = 0.743662
Epoch 15
Validation auc = 0.761033
Epoch 16
Validation auc = 0.779343
Epoch 17
Validation auc = 0.779343
Epoch 18
Validation auc = 0.783568
Epoch 19
Loss = 1.1853e-02, PNorm = 43.8333, GNorm = 2.2825, lr_0 = 9.8045e-04
Validation auc = 0.772770
Epoch 20
Validation auc = 0.764319
Epoch 21
Validation auc = 0.766197
Epoch 22
Validation auc = 0.753991
Epoch 23
Validation auc = 0.742254
Epoch 24
Loss = 1.1483e-02, PNorm = 43.8875, GNorm = 2.6067, lr_0 = 9.7207e-04
Validation auc = 0.741784
Epoch 25
Validation auc = 0.731455
Epoch 26
Validation auc = 0.731455
Epoch 27
Validation auc = 0.727230
Epoch 28
Validation auc = 0.723474
Epoch 29
Loss = 7.7149e-03, PNorm = 43.9435, GNorm = 2.2044, lr_0 = 9.6376e-04
Validation auc = 0.722535
Epoch 30
Validation auc = 0.738498
Epoch 31
Validation auc = 0.740845
Epoch 32
Validation auc = 0.727230
Epoch 33
Validation auc = 0.717840
Epoch 34
Loss = 6.6400e-03, PNorm = 43.9986, GNorm = 1.3607, lr_0 = 9.5552e-04
Validation auc = 0.715962
Epoch 35
Validation auc = 0.711737
Epoch 36
Validation auc = 0.701878
Epoch 37
Validation auc = 0.700469
Epoch 38
Validation auc = 0.692958
Epoch 39
Loss = 8.1273e-03, PNorm = 44.0598, GNorm = 1.9796, lr_0 = 9.4735e-04
Validation auc = 0.689202
Epoch 40
Validation auc = 0.686385
Epoch 41
Validation auc = 0.691549
Epoch 42
Validation auc = 0.706573
Epoch 43
Validation auc = 0.721127
Epoch 44
Loss = 7.9455e-03, PNorm = 44.1266, GNorm = 1.9946, lr_0 = 9.3925e-04
Validation auc = 0.723944
Epoch 45
Validation auc = 0.723005
Epoch 46
Validation auc = 0.707042
Epoch 47
Validation auc = 0.696714
Epoch 48
Validation auc = 0.694366
Epoch 49
Loss = 8.4831e-03, PNorm = 44.2073, GNorm = 3.0720, lr_0 = 9.3122e-04
Validation auc = 0.696244
Epoch 50
Validation auc = 0.701408
Epoch 51
Validation auc = 0.702347
Epoch 52
Validation auc = 0.698122
Epoch 53
Validation auc = 0.695305
Epoch 54
Loss = 6.3951e-03, PNorm = 44.2983, GNorm = 1.8096, lr_0 = 9.2326e-04
Validation auc = 0.688732
Epoch 55
Validation auc = 0.692488
Epoch 56
Validation auc = 0.688732
Epoch 57
Validation auc = 0.687793
Epoch 58
Validation auc = 0.684977
Epoch 59
Loss = 4.8472e-03, PNorm = 44.3893, GNorm = 1.3210, lr_0 = 9.1537e-04
Validation auc = 0.687793
Epoch 60
Validation auc = 0.696714
Epoch 61
Validation auc = 0.702817
Epoch 62
Validation auc = 0.713146
Epoch 63
Validation auc = 0.717840
Epoch 64
Loss = 5.6239e-03, PNorm = 44.4827, GNorm = 1.7999, lr_0 = 9.0754e-04
Validation auc = 0.720188
Epoch 65
Validation auc = 0.724413
Epoch 66
Validation auc = 0.724413
Epoch 67
Validation auc = 0.734742
Epoch 68
Validation auc = 0.723944
Epoch 69
Loss = 8.3305e-03, PNorm = 44.5700, GNorm = 2.8278, lr_0 = 8.9978e-04
Validation auc = 0.722066
Epoch 70
Validation auc = 0.715023
Epoch 71
Validation auc = 0.713615
Epoch 72
Validation auc = 0.705634
Epoch 73
Validation auc = 0.700939
Epoch 74
Loss = 4.6516e-03, PNorm = 44.6769, GNorm = 1.8631, lr_0 = 8.9209e-04
Validation auc = 0.690610
Epoch 75
Validation auc = 0.702817
Epoch 76
Validation auc = 0.708920
Epoch 77
Validation auc = 0.710329
Epoch 78
Validation auc = 0.716901
Epoch 79
Loss = 4.0539e-03, PNorm = 44.7733, GNorm = 1.6091, lr_0 = 8.8447e-04
Validation auc = 0.724413
Epoch 80
Validation auc = 0.732394
Epoch 81
Validation auc = 0.733333
Epoch 82
Validation auc = 0.734272
Epoch 83
Validation auc = 0.727700
Epoch 84
Loss = 6.0304e-03, PNorm = 44.8828, GNorm = 1.9344, lr_0 = 8.7691e-04
Validation auc = 0.713615
Epoch 85
Validation auc = 0.702347
Epoch 86
Validation auc = 0.697653
Epoch 87
Validation auc = 0.692019
Epoch 88
Validation auc = 0.694836
Epoch 89
Loss = 4.4240e-03, PNorm = 45.0088, GNorm = 1.3996, lr_0 = 8.6941e-04
Validation auc = 0.708451
Epoch 90
Validation auc = 0.710329
Epoch 91
Validation auc = 0.723944
Epoch 92
Validation auc = 0.733803
Epoch 93
Validation auc = 0.734272
Epoch 94
Loss = 6.6391e-03, PNorm = 45.1272, GNorm = 2.4306, lr_0 = 8.6198e-04
Validation auc = 0.734742
Epoch 95
Validation auc = 0.715023
Epoch 96
Validation auc = 0.727230
Epoch 97
Validation auc = 0.721596
Epoch 98
Validation auc = 0.708920
Epoch 99
Loss = 5.6179e-03, PNorm = 45.2366, GNorm = 2.8845, lr_0 = 8.5461e-04
Validation auc = 0.715493
Epoch 100
Validation auc = 0.729108
Epoch 101
Validation auc = 0.731925
Epoch 102
Validation auc = 0.733333
Epoch 103
Validation auc = 0.722535
Epoch 104
Loss = 5.4958e-03, PNorm = 45.3500, GNorm = 3.5590, lr_0 = 8.4730e-04
Validation auc = 0.714554
Epoch 105
Validation auc = 0.705634
Epoch 106
Validation auc = 0.702817
Epoch 107
Validation auc = 0.703286
Epoch 108
Validation auc = 0.714554
Epoch 109
Loss = 4.0000e-03, PNorm = 45.4533, GNorm = 1.6913, lr_0 = 8.4006e-04
Validation auc = 0.723944
Epoch 110
Validation auc = 0.733333
Epoch 111
Validation auc = 0.743192
Epoch 112
Validation auc = 0.745070
Epoch 113
Validation auc = 0.738498
Epoch 114
Loss = 4.1855e-03, PNorm = 45.5625, GNorm = 2.2394, lr_0 = 8.3288e-04
Validation auc = 0.730047
Epoch 115
Validation auc = 0.720188
Epoch 116
Validation auc = 0.721127
Epoch 117
Validation auc = 0.717840
Epoch 118
Validation auc = 0.715023
Epoch 119
Loss = 3.5226e-03, PNorm = 45.6583, GNorm = 1.4772, lr_0 = 8.2576e-04
Validation auc = 0.714085
Epoch 120
Validation auc = 0.728169
Epoch 121
Validation auc = 0.729577
Epoch 122
Validation auc = 0.729108
Epoch 123
Validation auc = 0.729577
Epoch 124
Loss = 2.9118e-03, PNorm = 45.7499, GNorm = 0.9274, lr_0 = 8.1870e-04
Validation auc = 0.726291
Epoch 125
Validation auc = 0.723944
Epoch 126
Validation auc = 0.723944
Epoch 127
Validation auc = 0.723474
Epoch 128
Validation auc = 0.716432
Epoch 129
Loss = 3.1261e-03, PNorm = 45.8597, GNorm = 2.4667, lr_0 = 8.1170e-04
Validation auc = 0.716432
Epoch 130
Validation auc = 0.725822
Epoch 131
Validation auc = 0.721127
Epoch 132
Validation auc = 0.719718
Epoch 133
Validation auc = 0.720188
Epoch 134
Loss = 2.3094e-03, PNorm = 45.9652, GNorm = 1.6757, lr_0 = 8.0476e-04
Validation auc = 0.726291
Epoch 135
Validation auc = 0.723944
Epoch 136
Validation auc = 0.723944
Epoch 137
Validation auc = 0.719249
Epoch 138
Validation auc = 0.722535
Epoch 139
Loss = 2.2645e-03, PNorm = 46.0525, GNorm = 1.2454, lr_0 = 7.9788e-04
Validation auc = 0.715962
Epoch 140
Validation auc = 0.720188
Epoch 141
Validation auc = 0.715023
Epoch 142
Validation auc = 0.709859
Epoch 143
Validation auc = 0.730516
Epoch 144
Loss = 3.3865e-03, PNorm = 46.1389, GNorm = 1.8647, lr_0 = 7.9106e-04
Validation auc = 0.722535
Epoch 145
Validation auc = 0.714554
Epoch 146
Validation auc = 0.722535
Epoch 147
Validation auc = 0.722535
Epoch 148
Validation auc = 0.721596
Epoch 149
Loss = 3.5596e-03, PNorm = 46.2213, GNorm = 2.2256, lr_0 = 7.8430e-04
Validation auc = 0.717840
Epoch 150
Validation auc = 0.703286
Epoch 151
Validation auc = 0.690610
Epoch 152
Validation auc = 0.693427
Epoch 153
Validation auc = 0.694366
Epoch 154
Loss = 1.1092e-03, PNorm = 46.3091, GNorm = 0.9416, lr_0 = 7.7759e-04
Validation auc = 0.698592
Epoch 155
Validation auc = 0.703286
Epoch 156
Validation auc = 0.714554
Epoch 157
Validation auc = 0.727230
Epoch 158
Validation auc = 0.727700
Epoch 159
Loss = 1.9815e-03, PNorm = 46.3785, GNorm = 2.1047, lr_0 = 7.7095e-04
Validation auc = 0.724883
Epoch 160
Validation auc = 0.731925
Epoch 161
Validation auc = 0.737559
Epoch 162
Validation auc = 0.736150
Epoch 163
Validation auc = 0.723474
Epoch 164
Loss = 2.7660e-03, PNorm = 46.4549, GNorm = 1.3578, lr_0 = 7.6436e-04
Validation auc = 0.718779
Epoch 165
Validation auc = 0.721127
Epoch 166
Validation auc = 0.723005
Epoch 167
Validation auc = 0.718310
Epoch 168
Validation auc = 0.701408
Epoch 169
Loss = 1.8138e-03, PNorm = 46.5359, GNorm = 1.3293, lr_0 = 7.5782e-04
Validation auc = 0.708920
Epoch 170
Validation auc = 0.720657
Epoch 171
Validation auc = 0.718779
Epoch 172
Validation auc = 0.703756
Epoch 173
Validation auc = 0.710329
Epoch 174
Loss = 1.9804e-03, PNorm = 46.5980, GNorm = 1.0966, lr_0 = 7.5134e-04
Validation auc = 0.715493
Epoch 175
Validation auc = 0.715493
Epoch 176
Validation auc = 0.723944
Epoch 177
Validation auc = 0.728169
Epoch 178
Validation auc = 0.731455
Epoch 179
Loss = 2.3718e-03, PNorm = 46.6762, GNorm = 2.2308, lr_0 = 7.4492e-04
Validation auc = 0.736620
Epoch 180
Validation auc = 0.732864
Epoch 181
Validation auc = 0.719718
Epoch 182
Validation auc = 0.707981
Epoch 183
Validation auc = 0.702347
Epoch 184
Loss = 2.3304e-03, PNorm = 46.7775, GNorm = 1.2445, lr_0 = 7.3855e-04
Validation auc = 0.691080
Epoch 185
Validation auc = 0.689202
Epoch 186
Validation auc = 0.688263
Epoch 187
Validation auc = 0.686854
Epoch 188
Validation auc = 0.692019
Epoch 189
Loss = 1.8398e-03, PNorm = 46.8561, GNorm = 1.5192, lr_0 = 7.3224e-04
Validation auc = 0.706103
Epoch 190
Validation auc = 0.700939
Epoch 191
Validation auc = 0.702817
Epoch 192
Validation auc = 0.706573
Epoch 193
Validation auc = 0.708920
Epoch 194
Loss = 1.6904e-03, PNorm = 46.9268, GNorm = 1.8079, lr_0 = 7.2598e-04
Validation auc = 0.710798
Epoch 195
Validation auc = 0.718779
Epoch 196
Validation auc = 0.727700
Epoch 197
Validation auc = 0.723474
Epoch 198
Validation auc = 0.719249
Epoch 199
Loss = 2.7395e-03, PNorm = 47.0028, GNorm = 2.4683, lr_0 = 7.1977e-04
Validation auc = 0.724413
Epoch 200
Validation auc = 0.725822
Epoch 201
Validation auc = 0.726761
Epoch 202
Validation auc = 0.734272
Epoch 203
Validation auc = 0.734272
Epoch 204
Loss = 1.4924e-03, PNorm = 47.0709, GNorm = 0.8793, lr_0 = 7.1362e-04
Validation auc = 0.730047
Epoch 205
Validation auc = 0.722066
Epoch 206
Validation auc = 0.722066
Epoch 207
Validation auc = 0.716901
Epoch 208
Validation auc = 0.710798
Epoch 209
Loss = 5.3764e-04, PNorm = 47.1425, GNorm = 0.5174, lr_0 = 7.0752e-04
Validation auc = 0.708451
Epoch 210
Validation auc = 0.708451
Epoch 211
Validation auc = 0.715962
Epoch 212
Validation auc = 0.718310
Epoch 213
Validation auc = 0.716432
Epoch 214
Loss = 7.7142e-04, PNorm = 47.2040, GNorm = 0.9043, lr_0 = 7.0147e-04
Validation auc = 0.713146
Epoch 215
Validation auc = 0.716901
Epoch 216
Validation auc = 0.729108
Epoch 217
Validation auc = 0.733803
Epoch 218
Validation auc = 0.735211
Epoch 219
Loss = 5.3064e-04, PNorm = 47.2554, GNorm = 0.2986, lr_0 = 6.9548e-04
Validation auc = 0.730986
Epoch 220
Validation auc = 0.730516
Epoch 221
Validation auc = 0.728169
Epoch 222
Validation auc = 0.722535
Epoch 223
Validation auc = 0.719718
Epoch 224
Loss = 2.1886e-03, PNorm = 47.3097, GNorm = 1.1810, lr_0 = 6.8953e-04
Validation auc = 0.715023
Epoch 225
Validation auc = 0.707512
Epoch 226
Validation auc = 0.686854
Epoch 227
Validation auc = 0.676995
Epoch 228
Validation auc = 0.679343
Epoch 229
Loss = 1.6495e-03, PNorm = 47.3666, GNorm = 1.3465, lr_0 = 6.8364e-04
Validation auc = 0.692958
Epoch 230
Validation auc = 0.688263
Epoch 231
Validation auc = 0.684977
Epoch 232
Validation auc = 0.689671
Epoch 233
Validation auc = 0.698592
Epoch 234
Loss = 2.3796e-03, PNorm = 47.4443, GNorm = 2.8839, lr_0 = 6.7779e-04
Validation auc = 0.708451
Epoch 235
Validation auc = 0.705164
Epoch 236
Validation auc = 0.707981
Epoch 237
Validation auc = 0.705634
Epoch 238
Validation auc = 0.704225
Epoch 239
Loss = 2.3112e-03, PNorm = 47.5018, GNorm = 0.7279, lr_0 = 6.7200e-04
Validation auc = 0.699061
Epoch 240
Validation auc = 0.695305
Epoch 241
Validation auc = 0.694366
Epoch 242
Validation auc = 0.693427
Epoch 243
Validation auc = 0.696244
Epoch 244
Loss = 1.5094e-04, PNorm = 47.5579, GNorm = 0.1268, lr_0 = 6.6625e-04
Validation auc = 0.696244
Epoch 245
Validation auc = 0.710329
Epoch 246
Validation auc = 0.720657
Epoch 247
Validation auc = 0.717840
Epoch 248
Validation auc = 0.716901
Epoch 249
Loss = 1.5760e-03, PNorm = 47.6056, GNorm = 1.4576, lr_0 = 6.6056e-04
Validation auc = 0.716432
Epoch 250
Validation auc = 0.716432
Epoch 251
Validation auc = 0.718779
Epoch 252
Validation auc = 0.721127
Epoch 253
Validation auc = 0.723005
Epoch 254
Loss = 9.0275e-04, PNorm = 47.6492, GNorm = 0.5069, lr_0 = 6.5491e-04
Validation auc = 0.719718
Epoch 255
Validation auc = 0.719249
Epoch 256
Validation auc = 0.717840
Epoch 257
Validation auc = 0.718310
Epoch 258
Validation auc = 0.719249
Epoch 259
Loss = 1.0144e-03, PNorm = 47.7018, GNorm = 1.2552, lr_0 = 6.4931e-04
Validation auc = 0.720188
Epoch 260
Validation auc = 0.716432
Epoch 261
Validation auc = 0.713146
Epoch 262
Validation auc = 0.717371
Epoch 263
Validation auc = 0.718779
Epoch 264
Loss = 5.1507e-04, PNorm = 47.7339, GNorm = 0.6741, lr_0 = 6.4376e-04
Validation auc = 0.723005
Epoch 265
Validation auc = 0.728169
Epoch 266
Validation auc = 0.726291
Epoch 267
Validation auc = 0.723474
Epoch 268
Validation auc = 0.717371
Epoch 269
Loss = 1.2273e-03, PNorm = 47.7895, GNorm = 2.4082, lr_0 = 6.3826e-04
Validation auc = 0.724413
Epoch 270
Validation auc = 0.730986
Epoch 271
Validation auc = 0.730047
Epoch 272
Validation auc = 0.726761
Epoch 273
Validation auc = 0.725822
Epoch 274
Loss = 2.5810e-03, PNorm = 47.8304, GNorm = 2.0877, lr_0 = 6.3280e-04
Validation auc = 0.724413
Epoch 275
Validation auc = 0.725352
Epoch 276
Validation auc = 0.722535
Epoch 277
Validation auc = 0.721596
Epoch 278
Validation auc = 0.717840
Epoch 279
Loss = 8.3320e-04, PNorm = 47.8940, GNorm = 1.2840, lr_0 = 6.2739e-04
Validation auc = 0.709390
Epoch 280
Validation auc = 0.705634
Epoch 281
Validation auc = 0.703286
Epoch 282
Validation auc = 0.702817
Epoch 283
Validation auc = 0.701408
Epoch 284
Loss = 2.0600e-03, PNorm = 47.9526, GNorm = 2.2145, lr_0 = 6.2203e-04
Validation auc = 0.695775
Epoch 285
Validation auc = 0.693897
Epoch 286
Validation auc = 0.692958
Epoch 287
Validation auc = 0.687793
Epoch 288
Validation auc = 0.687324
Epoch 289
Loss = 5.8736e-04, PNorm = 47.9920, GNorm = 0.9405, lr_0 = 6.1671e-04
Validation auc = 0.689202
Epoch 290
Validation auc = 0.691549
Epoch 291
Validation auc = 0.691080
Epoch 292
Validation auc = 0.687793
Epoch 293
Validation auc = 0.676995
Epoch 294
Loss = 7.6142e-04, PNorm = 48.0402, GNorm = 0.9809, lr_0 = 6.1144e-04
Validation auc = 0.679343
Epoch 295
Validation auc = 0.685446
Epoch 296
Validation auc = 0.689671
Epoch 297
Validation auc = 0.688732
Epoch 298
Validation auc = 0.691080
Epoch 299
Loss = 1.4591e-04, PNorm = 48.0878, GNorm = 0.1207, lr_0 = 6.0621e-04
Validation auc = 0.692958
Model 0 best validation auc = 0.810329 on epoch 8
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.889825
Ensemble test auc = 0.889825
Fold 6
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': 300,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': 1,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_6',
 'save_smiles_splits': False,
 'seed': 6,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': ['sars_cov_two_cl_protease_active'],
 'test': False,
 'test_fold_index': None,
 'train_data_size': 485,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 6
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.736620
Best score so far is 0.736620 at epoch 0 
Epoch 1
Validation auc = 0.762441
Best score so far is 0.762441 at epoch 1 
Epoch 2
Validation auc = 0.770423
Best score so far is 0.770423 at epoch 2 
Epoch 3
Validation auc = 0.784038
Best score so far is 0.784038 at epoch 3 
Epoch 4
Loss = 1.4752e-02, PNorm = 43.6374, GNorm = 4.4259, lr_0 = 6.5000e-04
Validation auc = 0.794366
Best score so far is 0.794366 at epoch 4 
Epoch 5
Validation auc = 0.806573
Best score so far is 0.806573 at epoch 5 
Epoch 6
Validation auc = 0.805164
Epoch 7
Validation auc = 0.801408
Epoch 8
Validation auc = 0.789671
Epoch 9
Loss = 1.1684e-02, PNorm = 43.6946, GNorm = 5.5458, lr_0 = 9.9743e-04
Validation auc = 0.770892
Epoch 10
Validation auc = 0.761972
Epoch 11
Validation auc = 0.775587
Epoch 12
Validation auc = 0.804695
Epoch 13
Validation auc = 0.807981
Best score so far is 0.807981 at epoch 13 
Epoch 14
Loss = 1.2121e-02, PNorm = 43.7646, GNorm = 3.1714, lr_0 = 9.8890e-04
Validation auc = 0.793427
Epoch 15
Validation auc = 0.767606
Epoch 16
Validation auc = 0.776526
Epoch 17
Validation auc = 0.761972
Epoch 18
Validation auc = 0.753991
Epoch 19
Loss = 9.5664e-03, PNorm = 43.8211, GNorm = 2.5124, lr_0 = 9.8045e-04
Validation auc = 0.748826
Epoch 20
Validation auc = 0.747418
Epoch 21
Validation auc = 0.762441
Epoch 22
Validation auc = 0.771831
Epoch 23
Validation auc = 0.769484
Epoch 24
Loss = 8.8161e-03, PNorm = 43.8711, GNorm = 2.8429, lr_0 = 9.7207e-04
Validation auc = 0.769484
Epoch 25
Validation auc = 0.773709
Epoch 26
Validation auc = 0.765728
Epoch 27
Validation auc = 0.743662
Epoch 28
Validation auc = 0.726291
Epoch 29
Loss = 7.9303e-03, PNorm = 43.9196, GNorm = 2.0698, lr_0 = 9.6376e-04
Validation auc = 0.716901
Epoch 30
Validation auc = 0.715023
Epoch 31
Validation auc = 0.721127
Epoch 32
Validation auc = 0.724883
Epoch 33
Validation auc = 0.722535
Epoch 34
Loss = 6.9843e-03, PNorm = 43.9666, GNorm = 1.8123, lr_0 = 9.5552e-04
Validation auc = 0.713146
Epoch 35
Validation auc = 0.698592
Epoch 36
Validation auc = 0.691549
Epoch 37
Validation auc = 0.694366
Epoch 38
Validation auc = 0.710798
Epoch 39
Loss = 8.6323e-03, PNorm = 44.0167, GNorm = 2.5384, lr_0 = 9.4735e-04
Validation auc = 0.723474
Epoch 40
Validation auc = 0.731925
Epoch 41
Validation auc = 0.741784
Epoch 42
Validation auc = 0.740376
Epoch 43
Validation auc = 0.734742
Epoch 44
Loss = 6.1737e-03, PNorm = 44.0741, GNorm = 2.0255, lr_0 = 9.3925e-04
Validation auc = 0.733333
Epoch 45
Validation auc = 0.724413
Epoch 46
Validation auc = 0.719718
Epoch 47
Validation auc = 0.714085
Epoch 48
Validation auc = 0.713146
Epoch 49
Loss = 6.0461e-03, PNorm = 44.1372, GNorm = 2.9898, lr_0 = 9.3122e-04
Validation auc = 0.718310
Epoch 50
Validation auc = 0.725352
Epoch 51
Validation auc = 0.708920
Epoch 52
Validation auc = 0.701878
Epoch 53
Validation auc = 0.703756
Epoch 54
Loss = 7.0465e-03, PNorm = 44.2103, GNorm = 1.9701, lr_0 = 9.2326e-04
Validation auc = 0.716901
Epoch 55
Validation auc = 0.723474
Epoch 56
Validation auc = 0.721127
Epoch 57
Validation auc = 0.719249
Epoch 58
Validation auc = 0.720657
Epoch 59
Loss = 6.2683e-03, PNorm = 44.2823, GNorm = 1.9200, lr_0 = 9.1537e-04
Validation auc = 0.722066
Epoch 60
Validation auc = 0.722535
Epoch 61
Validation auc = 0.724883
Epoch 62
Validation auc = 0.728169
Epoch 63
Validation auc = 0.739437
Epoch 64
Loss = 7.2418e-03, PNorm = 44.3565, GNorm = 2.4153, lr_0 = 9.0754e-04
Validation auc = 0.746009
Epoch 65
Validation auc = 0.739906
Epoch 66
Validation auc = 0.742723
Epoch 67
Validation auc = 0.741784
Epoch 68
Validation auc = 0.744601
Epoch 69
Loss = 5.8202e-03, PNorm = 44.4420, GNorm = 1.9766, lr_0 = 8.9978e-04
Validation auc = 0.746479
Epoch 70
Validation auc = 0.743662
Epoch 71
Validation auc = 0.738028
Epoch 72
Validation auc = 0.719718
Epoch 73
Validation auc = 0.708451
Epoch 74
Loss = 5.3793e-03, PNorm = 44.5503, GNorm = 1.7281, lr_0 = 8.9209e-04
Validation auc = 0.703756
Epoch 75
Validation auc = 0.707512
Epoch 76
Validation auc = 0.709859
Epoch 77
Validation auc = 0.720657
Epoch 78
Validation auc = 0.734742
Epoch 79
Loss = 4.3577e-03, PNorm = 44.6453, GNorm = 1.8337, lr_0 = 8.8447e-04
Validation auc = 0.750235
Epoch 80
Validation auc = 0.759155
Epoch 81
Validation auc = 0.750704
Epoch 82
Validation auc = 0.738028
Epoch 83
Validation auc = 0.726761
Epoch 84
Loss = 4.8723e-03, PNorm = 44.7528, GNorm = 2.3619, lr_0 = 8.7691e-04
Validation auc = 0.729577
Epoch 85
Validation auc = 0.721127
Epoch 86
Validation auc = 0.721127
Epoch 87
Validation auc = 0.730986
Epoch 88
Validation auc = 0.723944
Epoch 89
Loss = 5.1005e-03, PNorm = 44.8489, GNorm = 2.5201, lr_0 = 8.6941e-04
Validation auc = 0.726291
Epoch 90
Validation auc = 0.732864
Epoch 91
Validation auc = 0.732864
Epoch 92
Validation auc = 0.735211
Epoch 93
Validation auc = 0.737559
Epoch 94
Loss = 4.3128e-03, PNorm = 44.9593, GNorm = 1.7145, lr_0 = 8.6198e-04
Validation auc = 0.740376
Epoch 95
Validation auc = 0.747887
Epoch 96
Validation auc = 0.745540
Epoch 97
Validation auc = 0.736150
Epoch 98
Validation auc = 0.731925
Epoch 99
Loss = 6.3685e-03, PNorm = 45.0675, GNorm = 2.7368, lr_0 = 8.5461e-04
Validation auc = 0.717371
Epoch 100
Validation auc = 0.716432
Epoch 101
Validation auc = 0.715023
Epoch 102
Validation auc = 0.710798
Epoch 103
Validation auc = 0.704225
Epoch 104
Loss = 3.0588e-03, PNorm = 45.1803, GNorm = 1.5405, lr_0 = 8.4730e-04
Validation auc = 0.702817
Epoch 105
Validation auc = 0.725822
Epoch 106
Validation auc = 0.743192
Epoch 107
Validation auc = 0.750235
Epoch 108
Validation auc = 0.753521
Epoch 109
Loss = 5.6401e-03, PNorm = 45.2993, GNorm = 2.5952, lr_0 = 8.4006e-04
Validation auc = 0.758685
Epoch 110
Validation auc = 0.755399
Epoch 111
Validation auc = 0.749765
Epoch 112
Validation auc = 0.734742
Epoch 113
Validation auc = 0.729577
Epoch 114
Loss = 3.1761e-03, PNorm = 45.4432, GNorm = 1.4274, lr_0 = 8.3288e-04
Validation auc = 0.719249
Epoch 115
Validation auc = 0.722066
Epoch 116
Validation auc = 0.716432
Epoch 117
Validation auc = 0.721596
Epoch 118
Validation auc = 0.727700
Epoch 119
Loss = 2.8917e-03, PNorm = 45.5491, GNorm = 1.5783, lr_0 = 8.2576e-04
Validation auc = 0.732394
Epoch 120
Validation auc = 0.730516
Epoch 121
Validation auc = 0.723474
Epoch 122
Validation auc = 0.738498
Epoch 123
Validation auc = 0.749765
Epoch 124
Loss = 4.2979e-03, PNorm = 45.6700, GNorm = 2.5249, lr_0 = 8.1870e-04
Validation auc = 0.748357
Epoch 125
Validation auc = 0.749296
Epoch 126
Validation auc = 0.745070
Epoch 127
Validation auc = 0.737559
Epoch 128
Validation auc = 0.721127
Epoch 129
Loss = 4.6285e-03, PNorm = 45.7810, GNorm = 2.1073, lr_0 = 8.1170e-04
Validation auc = 0.714085
Epoch 130
Validation auc = 0.696714
Epoch 131
Validation auc = 0.689671
Epoch 132
Validation auc = 0.697183
Epoch 133
Validation auc = 0.716901
Epoch 134
Loss = 2.2643e-03, PNorm = 45.8838, GNorm = 1.5207, lr_0 = 8.0476e-04
Validation auc = 0.727230
Epoch 135
Validation auc = 0.733333
Epoch 136
Validation auc = 0.744601
Epoch 137
Validation auc = 0.747418
Epoch 138
Validation auc = 0.749765
Epoch 139
Loss = 4.6503e-03, PNorm = 45.9900, GNorm = 1.4445, lr_0 = 7.9788e-04
Validation auc = 0.741315
Epoch 140
Validation auc = 0.732394
Epoch 141
Validation auc = 0.742254
Epoch 142
Validation auc = 0.744131
Epoch 143
Validation auc = 0.734272
Epoch 144
Loss = 2.4411e-03, PNorm = 46.1074, GNorm = 1.5049, lr_0 = 7.9106e-04
Validation auc = 0.720657
Epoch 145
Validation auc = 0.721127
Epoch 146
Validation auc = 0.717840
Epoch 147
Validation auc = 0.724413
Epoch 148
Validation auc = 0.736620
Epoch 149
Loss = 2.8557e-03, PNorm = 46.2253, GNorm = 1.2294, lr_0 = 7.8430e-04
Validation auc = 0.738498
Epoch 150
Validation auc = 0.737089
Epoch 151
Validation auc = 0.727700
Epoch 152
Validation auc = 0.705634
Epoch 153
Validation auc = 0.715023
Epoch 154
Loss = 2.9790e-03, PNorm = 46.3293, GNorm = 2.8916, lr_0 = 7.7759e-04
Validation auc = 0.720657
Epoch 155
Validation auc = 0.721127
Epoch 156
Validation auc = 0.732394
Epoch 157
Validation auc = 0.735681
Epoch 158
Validation auc = 0.731925
Epoch 159
Loss = 1.9213e-03, PNorm = 46.4318, GNorm = 1.7475, lr_0 = 7.7095e-04
Validation auc = 0.725352
Epoch 160
Validation auc = 0.734272
Epoch 161
Validation auc = 0.733333
Epoch 162
Validation auc = 0.716901
Epoch 163
Validation auc = 0.705634
Epoch 164
Loss = 8.0349e-04, PNorm = 46.5426, GNorm = 0.5879, lr_0 = 7.6436e-04
Validation auc = 0.723944
Epoch 165
Validation auc = 0.723005
Epoch 166
Validation auc = 0.722535
Epoch 167
Validation auc = 0.721596
Epoch 168
Validation auc = 0.720188
Epoch 169
Loss = 1.2965e-03, PNorm = 46.6424, GNorm = 0.3977, lr_0 = 7.5782e-04
Validation auc = 0.707981
Epoch 170
Validation auc = 0.711737
Epoch 171
Validation auc = 0.726761
Epoch 172
Validation auc = 0.729577
Epoch 173
Validation auc = 0.730047
Epoch 174
Loss = 2.7863e-03, PNorm = 46.7297, GNorm = 1.8197, lr_0 = 7.5134e-04
Validation auc = 0.725822
Epoch 175
Validation auc = 0.727230
Epoch 176
Validation auc = 0.713146
Epoch 177
Validation auc = 0.715962
Epoch 178
Validation auc = 0.728169
Epoch 179
Loss = 1.3894e-03, PNorm = 46.8153, GNorm = 1.7811, lr_0 = 7.4492e-04
Validation auc = 0.726761
Epoch 180
Validation auc = 0.723005
Epoch 181
Validation auc = 0.718310
Epoch 182
Validation auc = 0.714554
Epoch 183
Validation auc = 0.716901
Epoch 184
Loss = 1.0338e-03, PNorm = 46.9214, GNorm = 0.6625, lr_0 = 7.3855e-04
Validation auc = 0.716432
Epoch 185
Validation auc = 0.719718
Epoch 186
Validation auc = 0.723474
Epoch 187
Validation auc = 0.728638
Epoch 188
Validation auc = 0.732864
Epoch 189
Loss = 6.6331e-04, PNorm = 46.9904, GNorm = 0.6544, lr_0 = 7.3224e-04
Validation auc = 0.730047
Epoch 190
Validation auc = 0.729577
Epoch 191
Validation auc = 0.731925
Epoch 192
Validation auc = 0.735211
Epoch 193
Validation auc = 0.736620
Epoch 194
Loss = 1.8173e-03, PNorm = 47.0771, GNorm = 1.8366, lr_0 = 7.2598e-04
Validation auc = 0.735211
Epoch 195
Validation auc = 0.708451
Epoch 196
Validation auc = 0.707981
Epoch 197
Validation auc = 0.707512
Epoch 198
Validation auc = 0.716901
Epoch 199
Loss = 6.3964e-04, PNorm = 47.1564, GNorm = 0.8143, lr_0 = 7.1977e-04
Validation auc = 0.718310
Epoch 200
Validation auc = 0.718779
Epoch 201
Validation auc = 0.715962
Epoch 202
Validation auc = 0.719718
Epoch 203
Validation auc = 0.715023
Epoch 204
Loss = 1.4370e-03, PNorm = 47.2210, GNorm = 0.8351, lr_0 = 7.1362e-04
Validation auc = 0.708451
Epoch 205
Validation auc = 0.706103
Epoch 206
Validation auc = 0.701408
Epoch 207
Validation auc = 0.703756
Epoch 208
Validation auc = 0.702347
Epoch 209
Loss = 5.0213e-04, PNorm = 47.2854, GNorm = 0.9453, lr_0 = 7.0752e-04
Validation auc = 0.699531
Epoch 210
Validation auc = 0.707981
Epoch 211
Validation auc = 0.711268
Epoch 212
Validation auc = 0.713615
Epoch 213
Validation auc = 0.710329
Epoch 214
Loss = 2.3784e-03, PNorm = 47.3439, GNorm = 1.7721, lr_0 = 7.0147e-04
Validation auc = 0.708451
Epoch 215
Validation auc = 0.710798
Epoch 216
Validation auc = 0.712207
Epoch 217
Validation auc = 0.710798
Epoch 218
Validation auc = 0.696714
Epoch 219
Loss = 3.9682e-04, PNorm = 47.3980, GNorm = 0.3851, lr_0 = 6.9548e-04
Validation auc = 0.681221
Epoch 220
Validation auc = 0.692488
Epoch 221
Validation auc = 0.709859
Epoch 222
Validation auc = 0.716901
Epoch 223
Validation auc = 0.713146
Epoch 224
Loss = 1.1536e-03, PNorm = 47.4590, GNorm = 0.6870, lr_0 = 6.8953e-04
Validation auc = 0.725352
Epoch 225
Validation auc = 0.735211
Epoch 226
Validation auc = 0.738028
Epoch 227
Validation auc = 0.739437
Epoch 228
Validation auc = 0.738028
Epoch 229
Loss = 4.9350e-04, PNorm = 47.5340, GNorm = 0.8045, lr_0 = 6.8364e-04
Validation auc = 0.734272
Epoch 230
Validation auc = 0.730047
Epoch 231
Validation auc = 0.728638
Epoch 232
Validation auc = 0.730986
Epoch 233
Validation auc = 0.723005
Epoch 234
Loss = 1.0840e-03, PNorm = 47.6087, GNorm = 1.6305, lr_0 = 6.7779e-04
Validation auc = 0.717371
Epoch 235
Validation auc = 0.716432
Epoch 236
Validation auc = 0.718310
Epoch 237
Validation auc = 0.711737
Epoch 238
Validation auc = 0.703286
Epoch 239
Loss = 2.4492e-03, PNorm = 47.6693, GNorm = 2.9850, lr_0 = 6.7200e-04
Validation auc = 0.705164
Epoch 240
Validation auc = 0.707981
Epoch 241
Validation auc = 0.712676
Epoch 242
Validation auc = 0.712676
Epoch 243
Validation auc = 0.717840
Epoch 244
Loss = 5.5246e-04, PNorm = 47.7330, GNorm = 0.1561, lr_0 = 6.6625e-04
Validation auc = 0.716901
Epoch 245
Validation auc = 0.723474
Epoch 246
Validation auc = 0.732394
Epoch 247
Validation auc = 0.734272
Epoch 248
Validation auc = 0.741784
Epoch 249
Loss = 5.3319e-04, PNorm = 47.7885, GNorm = 1.2356, lr_0 = 6.6056e-04
Validation auc = 0.746479
Epoch 250
Validation auc = 0.745540
Epoch 251
Validation auc = 0.745540
Epoch 252
Validation auc = 0.742254
Epoch 253
Validation auc = 0.731455
Epoch 254
Loss = 1.2162e-03, PNorm = 47.8445, GNorm = 2.1658, lr_0 = 6.5491e-04
Validation auc = 0.734742
Epoch 255
Validation auc = 0.745540
Epoch 256
Validation auc = 0.744601
Epoch 257
Validation auc = 0.743662
Epoch 258
Validation auc = 0.733333
Epoch 259
Loss = 4.1149e-04, PNorm = 47.8911, GNorm = 0.4025, lr_0 = 6.4931e-04
Validation auc = 0.725352
Epoch 260
Validation auc = 0.719249
Epoch 261
Validation auc = 0.713146
Epoch 262
Validation auc = 0.713615
Epoch 263
Validation auc = 0.708920
Epoch 264
Loss = 1.0121e-03, PNorm = 47.9452, GNorm = 0.8754, lr_0 = 6.4376e-04
Validation auc = 0.706573
Epoch 265
Validation auc = 0.712207
Epoch 266
Validation auc = 0.715023
Epoch 267
Validation auc = 0.715023
Epoch 268
Validation auc = 0.715023
Epoch 269
Loss = 1.8903e-03, PNorm = 48.0005, GNorm = 3.7877, lr_0 = 6.3826e-04
Validation auc = 0.707512
Epoch 270
Validation auc = 0.704695
Epoch 271
Validation auc = 0.702347
Epoch 272
Validation auc = 0.707042
Epoch 273
Validation auc = 0.704225
Epoch 274
Loss = 2.0432e-03, PNorm = 48.0437, GNorm = 1.9558, lr_0 = 6.3280e-04
Validation auc = 0.707042
Epoch 275
Validation auc = 0.706103
Epoch 276
Validation auc = 0.708920
Epoch 277
Validation auc = 0.702347
Epoch 278
Validation auc = 0.700939
Epoch 279
Loss = 1.2072e-03, PNorm = 48.0867, GNorm = 0.6331, lr_0 = 6.2739e-04
Validation auc = 0.699531
Epoch 280
Validation auc = 0.699061
Epoch 281
Validation auc = 0.699531
Epoch 282
Validation auc = 0.702347
Epoch 283
Validation auc = 0.703286
Epoch 284
Loss = 2.6352e-04, PNorm = 48.1242, GNorm = 0.3112, lr_0 = 6.2203e-04
Validation auc = 0.707042
Epoch 285
Validation auc = 0.707042
Epoch 286
Validation auc = 0.707042
Epoch 287
Validation auc = 0.710329
Epoch 288
Validation auc = 0.713146
Epoch 289
Loss = 4.6915e-04, PNorm = 48.1556, GNorm = 1.1565, lr_0 = 6.1671e-04
Validation auc = 0.715023
Epoch 290
Validation auc = 0.709390
Epoch 291
Validation auc = 0.700000
Epoch 292
Validation auc = 0.691549
Epoch 293
Validation auc = 0.683099
Epoch 294
Loss = 9.1464e-04, PNorm = 48.2016, GNorm = 1.0658, lr_0 = 6.1144e-04
Validation auc = 0.678873
Epoch 295
Validation auc = 0.669484
Epoch 296
Validation auc = 0.663380
Epoch 297
Validation auc = 0.669014
Epoch 298
Validation auc = 0.680282
Epoch 299
Loss = 9.5879e-04, PNorm = 48.2384, GNorm = 1.9482, lr_0 = 6.0621e-04
Validation auc = 0.688732
Model 0 best validation auc = 0.807981 on epoch 13
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.934377
Ensemble test auc = 0.934377
Fold 7
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': 300,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': 1,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_7',
 'save_smiles_splits': False,
 'seed': 7,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': ['sars_cov_two_cl_protease_active'],
 'test': False,
 'test_fold_index': None,
 'train_data_size': 485,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 7
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.752113
Best score so far is 0.752113 at epoch 0 
Epoch 1
Validation auc = 0.787324
Best score so far is 0.787324 at epoch 1 
Epoch 2
Validation auc = 0.801408
Best score so far is 0.801408 at epoch 2 
Epoch 3
Validation auc = 0.801408
Epoch 4
Loss = 1.8880e-02, PNorm = 43.6380, GNorm = 5.3101, lr_0 = 6.5000e-04
Validation auc = 0.819249
Best score so far is 0.819249 at epoch 4 
Epoch 5
Validation auc = 0.822535
Best score so far is 0.822535 at epoch 5 
Epoch 6
Validation auc = 0.818779
Epoch 7
Validation auc = 0.807512
Epoch 8
Validation auc = 0.749765
Epoch 9
Loss = 9.3576e-03, PNorm = 43.6908, GNorm = 3.8976, lr_0 = 9.9743e-04
Validation auc = 0.735211
Epoch 10
Validation auc = 0.750704
Epoch 11
Validation auc = 0.750235
Epoch 12
Validation auc = 0.755869
Epoch 13
Validation auc = 0.775587
Epoch 14
Loss = 7.9920e-03, PNorm = 43.7618, GNorm = 2.0825, lr_0 = 9.8890e-04
Validation auc = 0.793427
Epoch 15
Validation auc = 0.803286
Epoch 16
Validation auc = 0.786385
Epoch 17
Validation auc = 0.772300
Epoch 18
Validation auc = 0.760563
Epoch 19
Loss = 9.1198e-03, PNorm = 43.8195, GNorm = 2.1197, lr_0 = 9.8045e-04
Validation auc = 0.755399
Epoch 20
Validation auc = 0.747418
Epoch 21
Validation auc = 0.745070
Epoch 22
Validation auc = 0.749765
Epoch 23
Validation auc = 0.763850
Epoch 24
Loss = 7.1817e-03, PNorm = 43.8734, GNorm = 1.8989, lr_0 = 9.7207e-04
Validation auc = 0.755399
Epoch 25
Validation auc = 0.755869
Epoch 26
Validation auc = 0.754460
Epoch 27
Validation auc = 0.754460
Epoch 28
Validation auc = 0.752113
Epoch 29
Loss = 7.0765e-03, PNorm = 43.9286, GNorm = 1.5436, lr_0 = 9.6376e-04
Validation auc = 0.750704
Epoch 30
Validation auc = 0.720657
Epoch 31
Validation auc = 0.696244
Epoch 32
Validation auc = 0.705634
Epoch 33
Validation auc = 0.716901
Epoch 34
Loss = 7.6379e-03, PNorm = 43.9857, GNorm = 1.7684, lr_0 = 9.5552e-04
Validation auc = 0.716901
Epoch 35
Validation auc = 0.714085
Epoch 36
Validation auc = 0.712676
Epoch 37
Validation auc = 0.717840
Epoch 38
Validation auc = 0.728169
Epoch 39
Loss = 7.3214e-03, PNorm = 44.0509, GNorm = 1.8239, lr_0 = 9.4735e-04
Validation auc = 0.748826
Epoch 40
Validation auc = 0.756338
Epoch 41
Validation auc = 0.768075
Epoch 42
Validation auc = 0.769953
Epoch 43
Validation auc = 0.758216
Epoch 44
Loss = 8.6371e-03, PNorm = 44.1216, GNorm = 3.7126, lr_0 = 9.3925e-04
Validation auc = 0.752582
Epoch 45
Validation auc = 0.747418
Epoch 46
Validation auc = 0.739437
Epoch 47
Validation auc = 0.734742
Epoch 48
Validation auc = 0.733333
Epoch 49
Loss = 5.7843e-03, PNorm = 44.1984, GNorm = 2.7270, lr_0 = 9.3122e-04
Validation auc = 0.735211
Epoch 50
Validation auc = 0.731455
Epoch 51
Validation auc = 0.734272
Epoch 52
Validation auc = 0.734272
Epoch 53
Validation auc = 0.717371
Epoch 54
Loss = 7.6020e-03, PNorm = 44.2743, GNorm = 2.4915, lr_0 = 9.2326e-04
Validation auc = 0.701878
Epoch 55
Validation auc = 0.698592
Epoch 56
Validation auc = 0.699061
Epoch 57
Validation auc = 0.696714
Epoch 58
Validation auc = 0.695775
Epoch 59
Loss = 7.6742e-03, PNorm = 44.3711, GNorm = 1.9066, lr_0 = 9.1537e-04
Validation auc = 0.690141
Epoch 60
Validation auc = 0.693897
Epoch 61
Validation auc = 0.692488
Epoch 62
Validation auc = 0.695305
Epoch 63
Validation auc = 0.707042
Epoch 64
Loss = 5.9865e-03, PNorm = 44.4500, GNorm = 2.5296, lr_0 = 9.0754e-04
Validation auc = 0.722066
Epoch 65
Validation auc = 0.732394
Epoch 66
Validation auc = 0.738028
Epoch 67
Validation auc = 0.737559
Epoch 68
Validation auc = 0.729577
Epoch 69
Loss = 5.4728e-03, PNorm = 44.5480, GNorm = 1.8311, lr_0 = 8.9978e-04
Validation auc = 0.718779
Epoch 70
Validation auc = 0.707042
Epoch 71
Validation auc = 0.701878
Epoch 72
Validation auc = 0.709859
Epoch 73
Validation auc = 0.721127
Epoch 74
Loss = 7.0548e-03, PNorm = 44.6400, GNorm = 4.6924, lr_0 = 8.9209e-04
Validation auc = 0.723944
Epoch 75
Validation auc = 0.729108
Epoch 76
Validation auc = 0.723944
Epoch 77
Validation auc = 0.718310
Epoch 78
Validation auc = 0.708451
Epoch 79
Loss = 7.0646e-03, PNorm = 44.7357, GNorm = 3.2774, lr_0 = 8.8447e-04
Validation auc = 0.707042
Epoch 80
Validation auc = 0.712676
Epoch 81
Validation auc = 0.721127
Epoch 82
Validation auc = 0.723474
Epoch 83
Validation auc = 0.736620
Epoch 84
Loss = 5.9200e-03, PNorm = 44.8207, GNorm = 2.9393, lr_0 = 8.7691e-04
Validation auc = 0.753521
Epoch 85
Validation auc = 0.760563
Epoch 86
Validation auc = 0.753991
Epoch 87
Validation auc = 0.746009
Epoch 88
Validation auc = 0.737559
Epoch 89
Loss = 4.7819e-03, PNorm = 44.9305, GNorm = 1.7315, lr_0 = 8.6941e-04
Validation auc = 0.734742
Epoch 90
Validation auc = 0.734272
Epoch 91
Validation auc = 0.733803
Epoch 92
Validation auc = 0.733333
Epoch 93
Validation auc = 0.735681
Epoch 94
Loss = 4.1492e-03, PNorm = 45.0317, GNorm = 2.8018, lr_0 = 8.6198e-04
Validation auc = 0.746948
Epoch 95
Validation auc = 0.749765
Epoch 96
Validation auc = 0.751643
Epoch 97
Validation auc = 0.750704
Epoch 98
Validation auc = 0.739437
Epoch 99
Loss = 4.9495e-03, PNorm = 45.1305, GNorm = 1.7629, lr_0 = 8.5461e-04
Validation auc = 0.722535
Epoch 100
Validation auc = 0.706573
Epoch 101
Validation auc = 0.698122
Epoch 102
Validation auc = 0.700939
Epoch 103
Validation auc = 0.700000
Epoch 104
Loss = 4.6484e-03, PNorm = 45.2367, GNorm = 1.0545, lr_0 = 8.4730e-04
Validation auc = 0.715962
Epoch 105
Validation auc = 0.724883
Epoch 106
Validation auc = 0.726291
Epoch 107
Validation auc = 0.725822
Epoch 108
Validation auc = 0.731455
Epoch 109
Loss = 3.1806e-03, PNorm = 45.3422, GNorm = 1.1367, lr_0 = 8.4006e-04
Validation auc = 0.740376
Epoch 110
Validation auc = 0.739437
Epoch 111
Validation auc = 0.738967
Epoch 112
Validation auc = 0.737559
Epoch 113
Validation auc = 0.733803
Epoch 114
Loss = 3.6063e-03, PNorm = 45.4562, GNorm = 1.4419, lr_0 = 8.3288e-04
Validation auc = 0.724413
Epoch 115
Validation auc = 0.723944
Epoch 116
Validation auc = 0.722066
Epoch 117
Validation auc = 0.707042
Epoch 118
Validation auc = 0.718779
Epoch 119
Loss = 3.5556e-03, PNorm = 45.5647, GNorm = 2.3005, lr_0 = 8.2576e-04
Validation auc = 0.729577
Epoch 120
Validation auc = 0.726291
Epoch 121
Validation auc = 0.728638
Epoch 122
Validation auc = 0.736620
Epoch 123
Validation auc = 0.741784
Epoch 124
Loss = 3.3791e-03, PNorm = 45.6688, GNorm = 1.0074, lr_0 = 8.1870e-04
Validation auc = 0.742723
Epoch 125
Validation auc = 0.736620
Epoch 126
Validation auc = 0.733333
Epoch 127
Validation auc = 0.727700
Epoch 128
Validation auc = 0.723944
Epoch 129
Loss = 3.2046e-03, PNorm = 45.7875, GNorm = 2.3527, lr_0 = 8.1170e-04
Validation auc = 0.717840
Epoch 130
Validation auc = 0.713615
Epoch 131
Validation auc = 0.718779
Epoch 132
Validation auc = 0.720188
Epoch 133
Validation auc = 0.713615
Epoch 134
Loss = 3.2859e-03, PNorm = 45.8804, GNorm = 1.5729, lr_0 = 8.0476e-04
Validation auc = 0.715493
Epoch 135
Validation auc = 0.721127
Epoch 136
Validation auc = 0.721127
Epoch 137
Validation auc = 0.710329
Epoch 138
Validation auc = 0.709859
Epoch 139
Loss = 3.7896e-03, PNorm = 45.9681, GNorm = 0.5748, lr_0 = 7.9788e-04
Validation auc = 0.718779
Epoch 140
Validation auc = 0.715023
Epoch 141
Validation auc = 0.713615
Epoch 142
Validation auc = 0.707981
Epoch 143
Validation auc = 0.711268
Epoch 144
Loss = 3.5587e-03, PNorm = 46.0770, GNorm = 3.8015, lr_0 = 7.9106e-04
Validation auc = 0.703756
Epoch 145
Validation auc = 0.703756
Epoch 146
Validation auc = 0.716901
Epoch 147
Validation auc = 0.721127
Epoch 148
Validation auc = 0.708920
Epoch 149
Loss = 3.5229e-03, PNorm = 46.1846, GNorm = 1.0564, lr_0 = 7.8430e-04
Validation auc = 0.694836
Epoch 150
Validation auc = 0.688732
Epoch 151
Validation auc = 0.690141
Epoch 152
Validation auc = 0.688263
Epoch 153
Validation auc = 0.694366
Epoch 154
Loss = 1.9261e-03, PNorm = 46.2990, GNorm = 1.2397, lr_0 = 7.7759e-04
Validation auc = 0.699531
Epoch 155
Validation auc = 0.708451
Epoch 156
Validation auc = 0.710329
Epoch 157
Validation auc = 0.705164
Epoch 158
Validation auc = 0.706573
Epoch 159
Loss = 2.9904e-03, PNorm = 46.3943, GNorm = 2.2060, lr_0 = 7.7095e-04
Validation auc = 0.704695
Epoch 160
Validation auc = 0.705634
Epoch 161
Validation auc = 0.714554
Epoch 162
Validation auc = 0.715962
Epoch 163
Validation auc = 0.713146
Epoch 164
Loss = 2.4034e-03, PNorm = 46.4998, GNorm = 2.2420, lr_0 = 7.6436e-04
Validation auc = 0.709859
Epoch 165
Validation auc = 0.709859
Epoch 166
Validation auc = 0.719718
Epoch 167
Validation auc = 0.713615
Epoch 168
Validation auc = 0.711737
Epoch 169
Loss = 3.9385e-03, PNorm = 46.5873, GNorm = 0.5680, lr_0 = 7.5782e-04
Validation auc = 0.712207
Epoch 170
Validation auc = 0.709859
Epoch 171
Validation auc = 0.707981
Epoch 172
Validation auc = 0.687793
Epoch 173
Validation auc = 0.673709
Epoch 174
Loss = 3.4650e-03, PNorm = 46.6898, GNorm = 1.7660, lr_0 = 7.5134e-04
Validation auc = 0.684507
Epoch 175
Validation auc = 0.696714
Epoch 176
Validation auc = 0.699061
Epoch 177
Validation auc = 0.698592
Epoch 178
Validation auc = 0.700000
Epoch 179
Loss = 2.1481e-03, PNorm = 46.8082, GNorm = 1.3371, lr_0 = 7.4492e-04
Validation auc = 0.699531
Epoch 180
Validation auc = 0.700000
Epoch 181
Validation auc = 0.700939
Epoch 182
Validation auc = 0.693427
Epoch 183
Validation auc = 0.680751
Epoch 184
Loss = 2.0212e-03, PNorm = 46.9095, GNorm = 1.8510, lr_0 = 7.3855e-04
Validation auc = 0.684507
Epoch 185
Validation auc = 0.689671
Epoch 186
Validation auc = 0.694366
Epoch 187
Validation auc = 0.691549
Epoch 188
Validation auc = 0.691080
Epoch 189
Loss = 7.1823e-04, PNorm = 47.0103, GNorm = 0.3816, lr_0 = 7.3224e-04
Validation auc = 0.687793
Epoch 190
Validation auc = 0.688263
Epoch 191
Validation auc = 0.689671
Epoch 192
Validation auc = 0.692958
Epoch 193
Validation auc = 0.691080
Epoch 194
Loss = 1.2716e-03, PNorm = 47.1150, GNorm = 0.9689, lr_0 = 7.2598e-04
Validation auc = 0.684507
Epoch 195
Validation auc = 0.684038
Epoch 196
Validation auc = 0.684038
Epoch 197
Validation auc = 0.690141
Epoch 198
Validation auc = 0.695775
Epoch 199
Loss = 2.6451e-03, PNorm = 47.2038, GNorm = 2.6572, lr_0 = 7.1977e-04
Validation auc = 0.692488
Epoch 200
Validation auc = 0.691549
Epoch 201
Validation auc = 0.686854
Epoch 202
Validation auc = 0.689202
Epoch 203
Validation auc = 0.700469
Epoch 204
Loss = 1.0610e-03, PNorm = 47.2735, GNorm = 1.5311, lr_0 = 7.1362e-04
Validation auc = 0.698592
Epoch 205
Validation auc = 0.698122
Epoch 206
Validation auc = 0.695305
Epoch 207
Validation auc = 0.696244
Epoch 208
Validation auc = 0.697183
Epoch 209
Loss = 1.7129e-03, PNorm = 47.3473, GNorm = 1.6887, lr_0 = 7.0752e-04
Validation auc = 0.697653
Epoch 210
Validation auc = 0.693427
Epoch 211
Validation auc = 0.692488
Epoch 212
Validation auc = 0.700469
Epoch 213
Validation auc = 0.699531
Epoch 214
Loss = 2.0104e-03, PNorm = 47.4292, GNorm = 1.6655, lr_0 = 7.0147e-04
Validation auc = 0.691549
Epoch 215
Validation auc = 0.684038
Epoch 216
Validation auc = 0.684977
Epoch 217
Validation auc = 0.694366
Epoch 218
Validation auc = 0.696714
Epoch 219
Loss = 1.1788e-03, PNorm = 47.4802, GNorm = 0.7985, lr_0 = 6.9548e-04
Validation auc = 0.699531
Epoch 220
Validation auc = 0.703756
Epoch 221
Validation auc = 0.711268
Epoch 222
Validation auc = 0.715023
Epoch 223
Validation auc = 0.715023
Epoch 224
Loss = 1.8423e-03, PNorm = 47.5427, GNorm = 1.3486, lr_0 = 6.8953e-04
Validation auc = 0.715493
Epoch 225
Validation auc = 0.717840
Epoch 226
Validation auc = 0.715962
Epoch 227
Validation auc = 0.709390
Epoch 228
Validation auc = 0.707981
Epoch 229
Loss = 9.3406e-04, PNorm = 47.6162, GNorm = 0.9009, lr_0 = 6.8364e-04
Validation auc = 0.701408
Epoch 230
Validation auc = 0.694836
Epoch 231
Validation auc = 0.685915
Epoch 232
Validation auc = 0.680751
Epoch 233
Validation auc = 0.683568
Epoch 234
Loss = 5.0075e-04, PNorm = 47.6870, GNorm = 0.5173, lr_0 = 6.7779e-04
Validation auc = 0.691549
Epoch 235
Validation auc = 0.692488
Epoch 236
Validation auc = 0.686385
Epoch 237
Validation auc = 0.684038
Epoch 238
Validation auc = 0.683099
Epoch 239
Loss = 1.0826e-03, PNorm = 47.7445, GNorm = 0.8900, lr_0 = 6.7200e-04
Validation auc = 0.685915
Epoch 240
Validation auc = 0.684507
Epoch 241
Validation auc = 0.679343
Epoch 242
Validation auc = 0.676056
Epoch 243
Validation auc = 0.684507
Epoch 244
Loss = 1.2958e-03, PNorm = 47.8026, GNorm = 1.3726, lr_0 = 6.6625e-04
Validation auc = 0.692019
Epoch 245
Validation auc = 0.696244
Epoch 246
Validation auc = 0.698592
Epoch 247
Validation auc = 0.700469
Epoch 248
Validation auc = 0.685915
Epoch 249
Loss = 1.2827e-03, PNorm = 47.8560, GNorm = 0.8170, lr_0 = 6.6056e-04
Validation auc = 0.680751
Epoch 250
Validation auc = 0.681221
Epoch 251
Validation auc = 0.679812
Epoch 252
Validation auc = 0.682629
Epoch 253
Validation auc = 0.685915
Epoch 254
Loss = 6.1012e-04, PNorm = 47.9142, GNorm = 0.5885, lr_0 = 6.5491e-04
Validation auc = 0.690610
Epoch 255
Validation auc = 0.692488
Epoch 256
Validation auc = 0.692958
Epoch 257
Validation auc = 0.692958
Epoch 258
Validation auc = 0.695775
Epoch 259
Loss = 9.8337e-04, PNorm = 47.9677, GNorm = 0.8542, lr_0 = 6.4931e-04
Validation auc = 0.695775
Epoch 260
Validation auc = 0.697653
Epoch 261
Validation auc = 0.694836
Epoch 262
Validation auc = 0.694836
Epoch 263
Validation auc = 0.695305
Epoch 264
Loss = 1.3647e-03, PNorm = 48.0209, GNorm = 1.9720, lr_0 = 6.4376e-04
Validation auc = 0.692958
Epoch 265
Validation auc = 0.693427
Epoch 266
Validation auc = 0.694836
Epoch 267
Validation auc = 0.692958
Epoch 268
Validation auc = 0.689202
Epoch 269
Loss = 1.1169e-03, PNorm = 48.0662, GNorm = 1.0690, lr_0 = 6.3826e-04
Validation auc = 0.692019
Epoch 270
Validation auc = 0.694836
Epoch 271
Validation auc = 0.694366
Epoch 272
Validation auc = 0.689671
Epoch 273
Validation auc = 0.687793
Epoch 274
Loss = 7.9774e-04, PNorm = 48.1139, GNorm = 0.8704, lr_0 = 6.3280e-04
Validation auc = 0.690610
Epoch 275
Validation auc = 0.694836
Epoch 276
Validation auc = 0.704695
Epoch 277
Validation auc = 0.707512
Epoch 278
Validation auc = 0.706573
Epoch 279
Loss = 5.1239e-04, PNorm = 48.1651, GNorm = 0.5716, lr_0 = 6.2739e-04
Validation auc = 0.704695
Epoch 280
Validation auc = 0.702347
Epoch 281
Validation auc = 0.702817
Epoch 282
Validation auc = 0.700000
Epoch 283
Validation auc = 0.701408
Epoch 284
Loss = 9.4510e-04, PNorm = 48.2102, GNorm = 1.3043, lr_0 = 6.2203e-04
Validation auc = 0.700000
Epoch 285
Validation auc = 0.700469
Epoch 286
Validation auc = 0.706103
Epoch 287
Validation auc = 0.708451
Epoch 288
Validation auc = 0.709859
Epoch 289
Loss = 6.2323e-04, PNorm = 48.2501, GNorm = 0.7238, lr_0 = 6.1671e-04
Validation auc = 0.707042
Epoch 290
Validation auc = 0.702817
Epoch 291
Validation auc = 0.699531
Epoch 292
Validation auc = 0.696244
Epoch 293
Validation auc = 0.695775
Epoch 294
Loss = 1.4907e-03, PNorm = 48.2944, GNorm = 2.5368, lr_0 = 6.1144e-04
Validation auc = 0.692488
Epoch 295
Validation auc = 0.688263
Epoch 296
Validation auc = 0.684038
Epoch 297
Validation auc = 0.689671
Epoch 298
Validation auc = 0.702817
Epoch 299
Loss = 9.2383e-04, PNorm = 48.3371, GNorm = 0.9777, lr_0 = 6.0621e-04
Validation auc = 0.708451
Model 0 best validation auc = 0.822535 on epoch 5
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.906683
Ensemble test auc = 0.906683
Fold 8
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': 300,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': 1,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_8',
 'save_smiles_splits': False,
 'seed': 8,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': ['sars_cov_two_cl_protease_active'],
 'test': False,
 'test_fold_index': None,
 'train_data_size': 485,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 8
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.730047
Best score so far is 0.730047 at epoch 0 
Epoch 1
Validation auc = 0.758685
Best score so far is 0.758685 at epoch 1 
Epoch 2
Validation auc = 0.764319
Best score so far is 0.764319 at epoch 2 
Epoch 3
Validation auc = 0.767136
Best score so far is 0.767136 at epoch 3 
Epoch 4
Loss = 1.4711e-02, PNorm = 43.6368, GNorm = 4.4851, lr_0 = 6.5000e-04
Validation auc = 0.780282
Best score so far is 0.780282 at epoch 4 
Epoch 5
Validation auc = 0.790610
Best score so far is 0.790610 at epoch 5 
Epoch 6
Validation auc = 0.789671
Epoch 7
Validation auc = 0.790141
Epoch 8
Validation auc = 0.791549
Best score so far is 0.791549 at epoch 8 
Epoch 9
Loss = 1.1646e-02, PNorm = 43.6948, GNorm = 3.3147, lr_0 = 9.9743e-04
Validation auc = 0.781221
Epoch 10
Validation auc = 0.763850
Epoch 11
Validation auc = 0.765258
Epoch 12
Validation auc = 0.766197
Epoch 13
Validation auc = 0.743192
Epoch 14
Loss = 1.0726e-02, PNorm = 43.7610, GNorm = 4.8127, lr_0 = 9.8890e-04
Validation auc = 0.737559
Epoch 15
Validation auc = 0.750704
Epoch 16
Validation auc = 0.764789
Epoch 17
Validation auc = 0.753521
Epoch 18
Validation auc = 0.724883
Epoch 19
Loss = 7.8807e-03, PNorm = 43.8191, GNorm = 2.0661, lr_0 = 9.8045e-04
Validation auc = 0.719249
Epoch 20
Validation auc = 0.717371
Epoch 21
Validation auc = 0.709859
Epoch 22
Validation auc = 0.712676
Epoch 23
Validation auc = 0.708920
Epoch 24
Loss = 9.2504e-03, PNorm = 43.8680, GNorm = 2.2313, lr_0 = 9.7207e-04
Validation auc = 0.711268
Epoch 25
Validation auc = 0.710798
Epoch 26
Validation auc = 0.710798
Epoch 27
Validation auc = 0.709859
Epoch 28
Validation auc = 0.701408
Epoch 29
Loss = 9.0337e-03, PNorm = 43.9142, GNorm = 2.1331, lr_0 = 9.6376e-04
Validation auc = 0.694366
Epoch 30
Validation auc = 0.686854
Epoch 31
Validation auc = 0.683568
Epoch 32
Validation auc = 0.683568
Epoch 33
Validation auc = 0.676995
Epoch 34
Loss = 8.3709e-03, PNorm = 43.9653, GNorm = 2.5510, lr_0 = 9.5552e-04
Validation auc = 0.676526
Epoch 35
Validation auc = 0.684038
Epoch 36
Validation auc = 0.691549
Epoch 37
Validation auc = 0.691080
Epoch 38
Validation auc = 0.692019
Epoch 39
Loss = 7.8815e-03, PNorm = 44.0223, GNorm = 2.4018, lr_0 = 9.4735e-04
Validation auc = 0.692958
Epoch 40
Validation auc = 0.700000
Epoch 41
Validation auc = 0.705164
Epoch 42
Validation auc = 0.712207
Epoch 43
Validation auc = 0.707981
Epoch 44
Loss = 7.6426e-03, PNorm = 44.0887, GNorm = 2.0046, lr_0 = 9.3925e-04
Validation auc = 0.701878
Epoch 45
Validation auc = 0.707981
Epoch 46
Validation auc = 0.711268
Epoch 47
Validation auc = 0.715023
Epoch 48
Validation auc = 0.717840
Epoch 49
Loss = 5.6899e-03, PNorm = 44.1500, GNorm = 1.5588, lr_0 = 9.3122e-04
Validation auc = 0.715962
Epoch 50
Validation auc = 0.712676
Epoch 51
Validation auc = 0.700469
Epoch 52
Validation auc = 0.692488
Epoch 53
Validation auc = 0.686854
Epoch 54
Loss = 6.1251e-03, PNorm = 44.2180, GNorm = 1.7174, lr_0 = 9.2326e-04
Validation auc = 0.687793
Epoch 55
Validation auc = 0.685915
Epoch 56
Validation auc = 0.682629
Epoch 57
Validation auc = 0.681221
Epoch 58
Validation auc = 0.693427
Epoch 59
Loss = 6.1953e-03, PNorm = 44.2880, GNorm = 1.5745, lr_0 = 9.1537e-04
Validation auc = 0.710329
Epoch 60
Validation auc = 0.716432
Epoch 61
Validation auc = 0.722066
Epoch 62
Validation auc = 0.715493
Epoch 63
Validation auc = 0.705164
Epoch 64
Loss = 5.5881e-03, PNorm = 44.3458, GNorm = 2.1451, lr_0 = 9.0754e-04
Validation auc = 0.686854
Epoch 65
Validation auc = 0.689671
Epoch 66
Validation auc = 0.689671
Epoch 67
Validation auc = 0.691080
Epoch 68
Validation auc = 0.689202
Epoch 69
Loss = 7.1417e-03, PNorm = 44.4306, GNorm = 1.7196, lr_0 = 8.9978e-04
Validation auc = 0.683568
Epoch 70
Validation auc = 0.686385
Epoch 71
Validation auc = 0.687793
Epoch 72
Validation auc = 0.693427
Epoch 73
Validation auc = 0.699061
Epoch 74
Loss = 4.0070e-03, PNorm = 44.5172, GNorm = 1.8764, lr_0 = 8.9209e-04
Validation auc = 0.710329
Epoch 75
Validation auc = 0.717840
Epoch 76
Validation auc = 0.719249
Epoch 77
Validation auc = 0.721596
Epoch 78
Validation auc = 0.706103
Epoch 79
Loss = 5.6962e-03, PNorm = 44.6135, GNorm = 2.4851, lr_0 = 8.8447e-04
Validation auc = 0.699061
Epoch 80
Validation auc = 0.703286
Epoch 81
Validation auc = 0.717840
Epoch 82
Validation auc = 0.722535
Epoch 83
Validation auc = 0.726291
Epoch 84
Loss = 6.0708e-03, PNorm = 44.6990, GNorm = 2.4926, lr_0 = 8.7691e-04
Validation auc = 0.727700
Epoch 85
Validation auc = 0.728169
Epoch 86
Validation auc = 0.728169
Epoch 87
Validation auc = 0.719718
Epoch 88
Validation auc = 0.716901
Epoch 89
Loss = 6.4369e-03, PNorm = 44.8199, GNorm = 3.5548, lr_0 = 8.6941e-04
Validation auc = 0.719249
Epoch 90
Validation auc = 0.719249
Epoch 91
Validation auc = 0.725822
Epoch 92
Validation auc = 0.727230
Epoch 93
Validation auc = 0.728638
Epoch 94
Loss = 7.4768e-03, PNorm = 44.9160, GNorm = 2.2786, lr_0 = 8.6198e-04
Validation auc = 0.715962
Epoch 95
Validation auc = 0.703286
Epoch 96
Validation auc = 0.701408
Epoch 97
Validation auc = 0.703286
Epoch 98
Validation auc = 0.712207
Epoch 99
Loss = 6.3896e-03, PNorm = 45.0172, GNorm = 1.9292, lr_0 = 8.5461e-04
Validation auc = 0.713615
Epoch 100
Validation auc = 0.711737
Epoch 101
Validation auc = 0.698122
Epoch 102
Validation auc = 0.700469
Epoch 103
Validation auc = 0.702347
Epoch 104
Loss = 4.8112e-03, PNorm = 45.1199, GNorm = 1.5151, lr_0 = 8.4730e-04
Validation auc = 0.715493
Epoch 105
Validation auc = 0.725822
Epoch 106
Validation auc = 0.737559
Epoch 107
Validation auc = 0.739437
Epoch 108
Validation auc = 0.733803
Epoch 109
Loss = 3.9846e-03, PNorm = 45.2166, GNorm = 1.1585, lr_0 = 8.4006e-04
Validation auc = 0.725822
Epoch 110
Validation auc = 0.723474
Epoch 111
Validation auc = 0.720188
Epoch 112
Validation auc = 0.723944
Epoch 113
Validation auc = 0.729108
Epoch 114
Loss = 8.1438e-03, PNorm = 45.3137, GNorm = 1.8879, lr_0 = 8.3288e-04
Validation auc = 0.735211
Epoch 115
Validation auc = 0.740845
Epoch 116
Validation auc = 0.735211
Epoch 117
Validation auc = 0.736150
Epoch 118
Validation auc = 0.736150
Epoch 119
Loss = 6.8895e-03, PNorm = 45.4118, GNorm = 2.5037, lr_0 = 8.2576e-04
Validation auc = 0.737559
Epoch 120
Validation auc = 0.733333
Epoch 121
Validation auc = 0.731455
Epoch 122
Validation auc = 0.723005
Epoch 123
Validation auc = 0.718779
Epoch 124
Loss = 3.8726e-03, PNorm = 45.5285, GNorm = 1.0085, lr_0 = 8.1870e-04
Validation auc = 0.715962
Epoch 125
Validation auc = 0.715493
Epoch 126
Validation auc = 0.718779
Epoch 127
Validation auc = 0.725352
Epoch 128
Validation auc = 0.732394
Epoch 129
Loss = 3.4842e-03, PNorm = 45.6313, GNorm = 1.3046, lr_0 = 8.1170e-04
Validation auc = 0.737559
Epoch 130
Validation auc = 0.739906
Epoch 131
Validation auc = 0.743192
Epoch 132
Validation auc = 0.746948
Epoch 133
Validation auc = 0.747418
Epoch 134
Loss = 3.1932e-03, PNorm = 45.7404, GNorm = 1.7519, lr_0 = 8.0476e-04
Validation auc = 0.733803
Epoch 135
Validation auc = 0.725352
Epoch 136
Validation auc = 0.731455
Epoch 137
Validation auc = 0.731925
Epoch 138
Validation auc = 0.728169
Epoch 139
Loss = 2.4462e-03, PNorm = 45.8586, GNorm = 1.9308, lr_0 = 7.9788e-04
Validation auc = 0.724413
Epoch 140
Validation auc = 0.743662
Epoch 141
Validation auc = 0.747887
Epoch 142
Validation auc = 0.747887
Epoch 143
Validation auc = 0.749296
Epoch 144
Loss = 2.9350e-03, PNorm = 45.9729, GNorm = 0.9192, lr_0 = 7.9106e-04
Validation auc = 0.745540
Epoch 145
Validation auc = 0.739906
Epoch 146
Validation auc = 0.735211
Epoch 147
Validation auc = 0.723944
Epoch 148
Validation auc = 0.720188
Epoch 149
Loss = 3.7149e-03, PNorm = 46.0869, GNorm = 2.5258, lr_0 = 7.8430e-04
Validation auc = 0.727700
Epoch 150
Validation auc = 0.737559
Epoch 151
Validation auc = 0.745070
Epoch 152
Validation auc = 0.739437
Epoch 153
Validation auc = 0.731925
Epoch 154
Loss = 2.2036e-03, PNorm = 46.2017, GNorm = 1.2237, lr_0 = 7.7759e-04
Validation auc = 0.728169
Epoch 155
Validation auc = 0.732864
Epoch 156
Validation auc = 0.735211
Epoch 157
Validation auc = 0.735681
Epoch 158
Validation auc = 0.737089
Epoch 159
Loss = 2.7884e-03, PNorm = 46.3214, GNorm = 1.7974, lr_0 = 7.7095e-04
Validation auc = 0.738498
Epoch 160
Validation auc = 0.732864
Epoch 161
Validation auc = 0.719249
Epoch 162
Validation auc = 0.713615
Epoch 163
Validation auc = 0.720188
Epoch 164
Loss = 2.3430e-03, PNorm = 46.4291, GNorm = 1.3638, lr_0 = 7.6436e-04
Validation auc = 0.726291
Epoch 165
Validation auc = 0.723944
Epoch 166
Validation auc = 0.721596
Epoch 167
Validation auc = 0.730516
Epoch 168
Validation auc = 0.738028
Epoch 169
Loss = 3.2354e-03, PNorm = 46.5380, GNorm = 2.6898, lr_0 = 7.5782e-04
Validation auc = 0.739437
Epoch 170
Validation auc = 0.735211
Epoch 171
Validation auc = 0.734272
Epoch 172
Validation auc = 0.740376
Epoch 173
Validation auc = 0.743192
Epoch 174
Loss = 2.6072e-03, PNorm = 46.6555, GNorm = 0.9848, lr_0 = 7.5134e-04
Validation auc = 0.745540
Epoch 175
Validation auc = 0.734742
Epoch 176
Validation auc = 0.701878
Epoch 177
Validation auc = 0.694366
Epoch 178
Validation auc = 0.705164
Epoch 179
Loss = 2.0007e-03, PNorm = 46.7457, GNorm = 1.7029, lr_0 = 7.4492e-04
Validation auc = 0.711268
Epoch 180
Validation auc = 0.709390
Epoch 181
Validation auc = 0.714554
Epoch 182
Validation auc = 0.714085
Epoch 183
Validation auc = 0.712207
Epoch 184
Loss = 2.5971e-03, PNorm = 46.8637, GNorm = 2.0735, lr_0 = 7.3855e-04
Validation auc = 0.714554
Epoch 185
Validation auc = 0.715962
Epoch 186
Validation auc = 0.705634
Epoch 187
Validation auc = 0.702817
Epoch 188
Validation auc = 0.704695
Epoch 189
Loss = 1.7846e-03, PNorm = 46.9714, GNorm = 1.1087, lr_0 = 7.3224e-04
Validation auc = 0.718779
Epoch 190
Validation auc = 0.717371
Epoch 191
Validation auc = 0.709390
Epoch 192
Validation auc = 0.711268
Epoch 193
Validation auc = 0.718310
Epoch 194
Loss = 1.2702e-03, PNorm = 47.0668, GNorm = 2.6508, lr_0 = 7.2598e-04
Validation auc = 0.721596
Epoch 195
Validation auc = 0.709859
Epoch 196
Validation auc = 0.708451
Epoch 197
Validation auc = 0.708451
Epoch 198
Validation auc = 0.709390
Epoch 199
Loss = 2.0354e-03, PNorm = 47.1673, GNorm = 1.1883, lr_0 = 7.1977e-04
Validation auc = 0.712676
Epoch 200
Validation auc = 0.727230
Epoch 201
Validation auc = 0.738498
Epoch 202
Validation auc = 0.742254
Epoch 203
Validation auc = 0.747418
Epoch 204
Loss = 4.4526e-04, PNorm = 47.2371, GNorm = 0.4275, lr_0 = 7.1362e-04
Validation auc = 0.758685
Epoch 205
Validation auc = 0.762441
Epoch 206
Validation auc = 0.756808
Epoch 207
Validation auc = 0.746479
Epoch 208
Validation auc = 0.738498
Epoch 209
Loss = 1.5883e-03, PNorm = 47.2995, GNorm = 1.0803, lr_0 = 7.0752e-04
Validation auc = 0.737559
Epoch 210
Validation auc = 0.742723
Epoch 211
Validation auc = 0.745070
Epoch 212
Validation auc = 0.749296
Epoch 213
Validation auc = 0.753052
Epoch 214
Loss = 1.2016e-03, PNorm = 47.3806, GNorm = 2.3299, lr_0 = 7.0147e-04
Validation auc = 0.756338
Epoch 215
Validation auc = 0.760094
Epoch 216
Validation auc = 0.761033
Epoch 217
Validation auc = 0.759155
Epoch 218
Validation auc = 0.757746
Epoch 219
Loss = 8.6067e-04, PNorm = 47.4561, GNorm = 0.9363, lr_0 = 6.9548e-04
Validation auc = 0.752113
Epoch 220
Validation auc = 0.746948
Epoch 221
Validation auc = 0.741315
Epoch 222
Validation auc = 0.734742
Epoch 223
Validation auc = 0.730047
Epoch 224
Loss = 5.4666e-04, PNorm = 47.5366, GNorm = 0.2907, lr_0 = 6.8953e-04
Validation auc = 0.724413
Epoch 225
Validation auc = 0.715493
Epoch 226
Validation auc = 0.718310
Epoch 227
Validation auc = 0.720188
Epoch 228
Validation auc = 0.736620
Epoch 229
Loss = 1.4297e-03, PNorm = 47.5979, GNorm = 0.8737, lr_0 = 6.8364e-04
Validation auc = 0.738967
Epoch 230
Validation auc = 0.734272
Epoch 231
Validation auc = 0.731455
Epoch 232
Validation auc = 0.728169
Epoch 233
Validation auc = 0.722066
Epoch 234
Loss = 1.0697e-03, PNorm = 47.6792, GNorm = 0.9509, lr_0 = 6.7779e-04
Validation auc = 0.716432
Epoch 235
Validation auc = 0.715493
Epoch 236
Validation auc = 0.713146
Epoch 237
Validation auc = 0.710329
Epoch 238
Validation auc = 0.716432
Epoch 239
Loss = 9.7535e-04, PNorm = 47.7603, GNorm = 1.2045, lr_0 = 6.7200e-04
Validation auc = 0.722535
Epoch 240
Validation auc = 0.726291
Epoch 241
Validation auc = 0.729108
Epoch 242
Validation auc = 0.726291
Epoch 243
Validation auc = 0.727700
Epoch 244
Loss = 1.2310e-03, PNorm = 47.8336, GNorm = 0.3852, lr_0 = 6.6625e-04
Validation auc = 0.731925
Epoch 245
Validation auc = 0.741315
Epoch 246
Validation auc = 0.742723
Epoch 247
Validation auc = 0.749765
Epoch 248
Validation auc = 0.747418
Epoch 249
Loss = 7.8132e-04, PNorm = 47.8946, GNorm = 0.9812, lr_0 = 6.6056e-04
Validation auc = 0.744601
Epoch 250
Validation auc = 0.740845
Epoch 251
Validation auc = 0.734742
Epoch 252
Validation auc = 0.737089
Epoch 253
Validation auc = 0.740376
Epoch 254
Loss = 9.4149e-04, PNorm = 47.9595, GNorm = 0.4596, lr_0 = 6.5491e-04
Validation auc = 0.737089
Epoch 255
Validation auc = 0.732394
Epoch 256
Validation auc = 0.728169
Epoch 257
Validation auc = 0.729108
Epoch 258
Validation auc = 0.747887
Epoch 259
Loss = 1.9867e-03, PNorm = 48.0254, GNorm = 2.3121, lr_0 = 6.4931e-04
Validation auc = 0.758216
Epoch 260
Validation auc = 0.758216
Epoch 261
Validation auc = 0.759155
Epoch 262
Validation auc = 0.759155
Epoch 263
Validation auc = 0.760563
Epoch 264
Loss = 1.7438e-03, PNorm = 48.1038, GNorm = 1.1942, lr_0 = 6.4376e-04
Validation auc = 0.757746
Epoch 265
Validation auc = 0.754930
Epoch 266
Validation auc = 0.749765
Epoch 267
Validation auc = 0.745540
Epoch 268
Validation auc = 0.738498
Epoch 269
Loss = 2.2889e-03, PNorm = 48.1735, GNorm = 1.9575, lr_0 = 6.3826e-04
Validation auc = 0.740376
Epoch 270
Validation auc = 0.745070
Epoch 271
Validation auc = 0.746948
Epoch 272
Validation auc = 0.748357
Epoch 273
Validation auc = 0.746948
Epoch 274
Loss = 4.6273e-04, PNorm = 48.2201, GNorm = 0.4820, lr_0 = 6.3280e-04
Validation auc = 0.744131
Epoch 275
Validation auc = 0.745540
Epoch 276
Validation auc = 0.744601
Epoch 277
Validation auc = 0.741784
Epoch 278
Validation auc = 0.742254
Epoch 279
Loss = 1.5050e-03, PNorm = 48.2665, GNorm = 1.6912, lr_0 = 6.2739e-04
Validation auc = 0.742723
Epoch 280
Validation auc = 0.740376
Epoch 281
Validation auc = 0.743192
Epoch 282
Validation auc = 0.738967
Epoch 283
Validation auc = 0.737559
Epoch 284
Loss = 9.8954e-04, PNorm = 48.3444, GNorm = 0.7974, lr_0 = 6.2203e-04
Validation auc = 0.738498
Epoch 285
Validation auc = 0.736620
Epoch 286
Validation auc = 0.731925
Epoch 287
Validation auc = 0.718310
Epoch 288
Validation auc = 0.708920
Epoch 289
Loss = 7.4138e-04, PNorm = 48.3932, GNorm = 1.4748, lr_0 = 6.1671e-04
Validation auc = 0.709390
Epoch 290
Validation auc = 0.715493
Epoch 291
Validation auc = 0.721127
Epoch 292
Validation auc = 0.727700
Epoch 293
Validation auc = 0.728638
Epoch 294
Loss = 3.0150e-03, PNorm = 48.4267, GNorm = 0.5301, lr_0 = 6.1144e-04
Validation auc = 0.726291
Epoch 295
Validation auc = 0.725352
Epoch 296
Validation auc = 0.724883
Epoch 297
Validation auc = 0.725352
Epoch 298
Validation auc = 0.720657
Epoch 299
Loss = 3.2263e-04, PNorm = 48.4709, GNorm = 0.5120, lr_0 = 6.0621e-04
Validation auc = 0.719718
Model 0 best validation auc = 0.791549 on epoch 8
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.937989
Ensemble test auc = 0.937989
Fold 9
Command line
python /home/saxelrod/Repo/projects/chemprop/train.py --config_path /home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json --data_path /home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv --dataset_type classification
Args
{'activation': 'ReLU',
 'atom_messages': False,
 'batch_size': 50,
 'bias': False,
 'cache_cutoff': 10000,
 'checkpoint_dir': None,
 'checkpoint_path': None,
 'checkpoint_paths': None,
 'class_balance': True,
 'config_path': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/config.json',
 'crossval_index_dir': None,
 'crossval_index_file': None,
 'crossval_index_sets': None,
 'cuda': True,
 'data_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/train_full.csv',
 'dataset_type': 'classification',
 'depth': 4,
 'device': device(type='cuda', index=0),
 'dropout': 0.25,
 'ensemble_size': 1,
 'epochs': 300,
 'features_generator': None,
 'features_only': False,
 'features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/train_auc.npz'],
 'features_scaling': False,
 'features_size': 300,
 'ffn_hidden_size': 500,
 'ffn_num_layers': 2,
 'final_lr': 0.0001,
 'folds_file': None,
 'gpu': 0,
 'hidden_size': 500,
 'init_lr': 0.0001,
 'log_frequency': 10,
 'max_data_size': None,
 'max_lr': 0.001,
 'metric': 'auc',
 'minimize_score': False,
 'multiclass_num_classes': 3,
 'no_cuda': False,
 'no_features_scaling': True,
 'num_folds': 10,
 'num_lrs': 1,
 'num_tasks': 1,
 'num_workers': 8,
 'pytorch_seed': 0,
 'quiet': True,
 'save_dir': '/home/saxelrod/chemprop_cov_2/models/fps_from_att_k1_yes_prob_feats_mpnn_from_auc/fold_9',
 'save_smiles_splits': False,
 'seed': 9,
 'separate_test_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/test_auc.npz'],
 'separate_test_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/test_full.csv',
 'separate_val_features_path': ['/home/saxelrod/chemprop_cov_2/features/fps_from_att_k1_yes_prob/val_auc.npz'],
 'separate_val_path': '/home/saxelrod/chemprop_cov_2/scaffold_split/val_full.csv',
 'show_individual_scores': False,
 'smiles_column': None,
 'split_sizes': (0.8, 0.1, 0.1),
 'split_type': 'random',
 'target_columns': None,
 'task_names': ['sars_cov_two_cl_protease_active'],
 'test': False,
 'test_fold_index': None,
 'train_data_size': 485,
 'undirected': False,
 'use_input_features': True,
 'val_fold_index': None,
 'warmup_epochs': 2.0}
Loading data
Number of tasks = 1
Splitting data with seed 9
Class sizes
sars_cov_two_cl_protease_active 0: 89.69%, 1: 10.31%
Total size = 485 | train size = 485 | val size = 157 | test size = 162
Building model 0
MoleculeModel(
  (sigmoid): Sigmoid()
  (encoder): MPN(
    (encoder): MPNEncoder(
      (dropout_layer): Dropout(p=0.25, inplace=False)
      (act_func): ReLU()
      (W_i): Linear(in_features=147, out_features=500, bias=False)
      (W_h): Linear(in_features=500, out_features=500, bias=False)
      (W_o): Linear(in_features=633, out_features=500, bias=True)
    )
  )
  (ffn): Sequential(
    (0): Dropout(p=0.25, inplace=False)
    (1): Linear(in_features=800, out_features=500, bias=True)
    (2): ReLU()
    (3): Dropout(p=0.25, inplace=False)
    (4): Linear(in_features=500, out_features=1, bias=True)
  )
)
Number of parameters = 1,041,501
Moving model to cuda
Epoch 0
Validation auc = 0.717371
Best score so far is 0.717371 at epoch 0 
Epoch 1
Validation auc = 0.772770
Best score so far is 0.772770 at epoch 1 
Epoch 2
Validation auc = 0.772300
Epoch 3
Validation auc = 0.777934
Best score so far is 0.777934 at epoch 3 
Epoch 4
Loss = 1.4037e-02, PNorm = 43.6375, GNorm = 4.7107, lr_0 = 6.5000e-04
Validation auc = 0.796244
Best score so far is 0.796244 at epoch 4 
Epoch 5
Validation auc = 0.817840
Best score so far is 0.817840 at epoch 5 
Epoch 6
Validation auc = 0.792488
Epoch 7
Validation auc = 0.794836
Epoch 8
Validation auc = 0.792958
Epoch 9
Loss = 1.0664e-02, PNorm = 43.6890, GNorm = 2.2804, lr_0 = 9.9743e-04
Validation auc = 0.781221
Epoch 10
Validation auc = 0.787793
Epoch 11
Validation auc = 0.791080
Epoch 12
Validation auc = 0.793897
Epoch 13
Validation auc = 0.788732
Epoch 14
Loss = 1.0175e-02, PNorm = 43.7548, GNorm = 3.6000, lr_0 = 9.8890e-04
Validation auc = 0.802347
Epoch 15
Validation auc = 0.801408
Epoch 16
Validation auc = 0.799531
Epoch 17
Validation auc = 0.786854
Epoch 18
Validation auc = 0.778873
Epoch 19
Loss = 7.6839e-03, PNorm = 43.8097, GNorm = 1.8576, lr_0 = 9.8045e-04
Validation auc = 0.782160
Epoch 20
Validation auc = 0.779812
Epoch 21
Validation auc = 0.774648
Epoch 22
Validation auc = 0.769014
Epoch 23
Validation auc = 0.769484
Epoch 24
Loss = 8.7878e-03, PNorm = 43.8562, GNorm = 1.9423, lr_0 = 9.7207e-04
Validation auc = 0.781690
Epoch 25
Validation auc = 0.784977
Epoch 26
Validation auc = 0.765728
Epoch 27
Validation auc = 0.753991
Epoch 28
Validation auc = 0.748826
Epoch 29
Loss = 8.7276e-03, PNorm = 43.9014, GNorm = 2.1453, lr_0 = 9.6376e-04
Validation auc = 0.741315
Epoch 30
Validation auc = 0.730986
Epoch 31
Validation auc = 0.719249
Epoch 32
Validation auc = 0.724883
Epoch 33
Validation auc = 0.729108
Epoch 34
Loss = 8.0386e-03, PNorm = 43.9488, GNorm = 2.1441, lr_0 = 9.5552e-04
Validation auc = 0.731925
Epoch 35
Validation auc = 0.729108
Epoch 36
Validation auc = 0.730986
Epoch 37
Validation auc = 0.732864
Epoch 38
Validation auc = 0.742254
Epoch 39
Loss = 8.6812e-03, PNorm = 44.0009, GNorm = 1.6808, lr_0 = 9.4735e-04
Validation auc = 0.741784
Epoch 40
Validation auc = 0.730047
Epoch 41
Validation auc = 0.723474
Epoch 42
Validation auc = 0.709859
Epoch 43
Validation auc = 0.708451
Epoch 44
Loss = 7.9891e-03, PNorm = 44.0666, GNorm = 1.8365, lr_0 = 9.3925e-04
Validation auc = 0.706103
Epoch 45
Validation auc = 0.700000
Epoch 46
Validation auc = 0.700469
Epoch 47
Validation auc = 0.718310
Epoch 48
Validation auc = 0.734272
Epoch 49
Loss = 5.9544e-03, PNorm = 44.1301, GNorm = 1.5397, lr_0 = 9.3122e-04
Validation auc = 0.747418
Epoch 50
Validation auc = 0.754930
Epoch 51
Validation auc = 0.754460
Epoch 52
Validation auc = 0.748826
Epoch 53
Validation auc = 0.738028
Epoch 54
Loss = 5.8486e-03, PNorm = 44.2063, GNorm = 2.1140, lr_0 = 9.2326e-04
Validation auc = 0.731925
Epoch 55
Validation auc = 0.733333
Epoch 56
Validation auc = 0.733333
Epoch 57
Validation auc = 0.726291
Epoch 58
Validation auc = 0.713146
Epoch 59
Loss = 5.9996e-03, PNorm = 44.2896, GNorm = 2.1192, lr_0 = 9.1537e-04
Validation auc = 0.710798
Epoch 60
Validation auc = 0.718310
Epoch 61
Validation auc = 0.725822
Epoch 62
Validation auc = 0.734272
Epoch 63
Validation auc = 0.741315
Epoch 64
Loss = 5.7154e-03, PNorm = 44.3819, GNorm = 1.3883, lr_0 = 9.0754e-04
Validation auc = 0.736150
Epoch 65
Validation auc = 0.719718
Epoch 66
Validation auc = 0.713615
Epoch 67
Validation auc = 0.697183
Epoch 68
Validation auc = 0.690141
Epoch 69
Loss = 5.0554e-03, PNorm = 44.4788, GNorm = 2.1865, lr_0 = 8.9978e-04
Validation auc = 0.693427
Epoch 70
Validation auc = 0.699061
Epoch 71
Validation auc = 0.710329
Epoch 72
Validation auc = 0.721127
Epoch 73
Validation auc = 0.730516
Epoch 74
Loss = 3.6675e-03, PNorm = 44.5746, GNorm = 1.2337, lr_0 = 8.9209e-04
Validation auc = 0.736620
Epoch 75
Validation auc = 0.740376
Epoch 76
Validation auc = 0.727700
Epoch 77
Validation auc = 0.702347
Epoch 78
Validation auc = 0.691549
Epoch 79
Loss = 5.8008e-03, PNorm = 44.6815, GNorm = 2.4972, lr_0 = 8.8447e-04
Validation auc = 0.696244
Epoch 80
Validation auc = 0.689202
Epoch 81
Validation auc = 0.708451
Epoch 82
Validation auc = 0.721596
Epoch 83
Validation auc = 0.722535
Epoch 84
Loss = 5.7836e-03, PNorm = 44.7643, GNorm = 2.1264, lr_0 = 8.7691e-04
Validation auc = 0.728169
Epoch 85
Validation auc = 0.742723
Epoch 86
Validation auc = 0.742254
Epoch 87
Validation auc = 0.731455
Epoch 88
Validation auc = 0.727230
Epoch 89
Loss = 5.3978e-03, PNorm = 44.8611, GNorm = 1.5213, lr_0 = 8.6941e-04
Validation auc = 0.732864
Epoch 90
Validation auc = 0.742723
Epoch 91
Validation auc = 0.740376
Epoch 92
Validation auc = 0.744131
Epoch 93
Validation auc = 0.747887
Epoch 94
Loss = 4.6301e-03, PNorm = 44.9692, GNorm = 1.7156, lr_0 = 8.6198e-04
Validation auc = 0.740845
Epoch 95
Validation auc = 0.750235
Epoch 96
Validation auc = 0.737089
Epoch 97
Validation auc = 0.737089
Epoch 98
Validation auc = 0.743662
Epoch 99
Loss = 5.4496e-03, PNorm = 45.0857, GNorm = 3.0553, lr_0 = 8.5461e-04
Validation auc = 0.750235
Epoch 100
Validation auc = 0.738028
Epoch 101
Validation auc = 0.749296
Epoch 102
Validation auc = 0.762441
Epoch 103
Validation auc = 0.753991
Epoch 104
Loss = 4.8296e-03, PNorm = 45.2044, GNorm = 2.6970, lr_0 = 8.4730e-04
Validation auc = 0.752113
Epoch 105
Validation auc = 0.752113
Epoch 106
Validation auc = 0.749296
Epoch 107
Validation auc = 0.742723
Epoch 108
Validation auc = 0.738967
Epoch 109
Loss = 3.3696e-03, PNorm = 45.3212, GNorm = 2.1607, lr_0 = 8.4006e-04
Validation auc = 0.741315
Epoch 110
Validation auc = 0.738498
Epoch 111
Validation auc = 0.738498
Epoch 112
Validation auc = 0.738028
Epoch 113
Validation auc = 0.738498
Epoch 114
Loss = 4.4430e-03, PNorm = 45.4304, GNorm = 1.6944, lr_0 = 8.3288e-04
Validation auc = 0.736620
Epoch 115
Validation auc = 0.733333
Epoch 116
Validation auc = 0.726761
Epoch 117
Validation auc = 0.722535
Epoch 118
Validation auc = 0.729108
Epoch 119
Loss = 2.6503e-03, PNorm = 45.5377, GNorm = 1.4834, lr_0 = 8.2576e-04
Validation auc = 0.730516
Epoch 120
Validation auc = 0.729108
Epoch 121
Validation auc = 0.724883
Epoch 122
Validation auc = 0.723005
Epoch 123
Validation auc = 0.716901
Epoch 124
Loss = 3.4396e-03, PNorm = 45.6532, GNorm = 2.9749, lr_0 = 8.1870e-04
Validation auc = 0.715023
Epoch 125
Validation auc = 0.722066
Epoch 126
Validation auc = 0.731925
Epoch 127
Validation auc = 0.733333
Epoch 128
Validation auc = 0.733333
Epoch 129
Loss = 1.8756e-03, PNorm = 45.7646, GNorm = 1.6632, lr_0 = 8.1170e-04
Validation auc = 0.740845
Epoch 130
Validation auc = 0.757277
Epoch 131
Validation auc = 0.748826
Epoch 132
Validation auc = 0.741784
Epoch 133
Validation auc = 0.736620
Epoch 134
Loss = 2.3000e-03, PNorm = 45.8728, GNorm = 0.9376, lr_0 = 8.0476e-04
Validation auc = 0.740845
Epoch 135
Validation auc = 0.731455
Epoch 136
Validation auc = 0.732864
Epoch 137
Validation auc = 0.753521
Epoch 138
Validation auc = 0.749765
Epoch 139
Loss = 3.2491e-03, PNorm = 45.9679, GNorm = 1.4308, lr_0 = 7.9788e-04
Validation auc = 0.749296
Epoch 140
Validation auc = 0.748357
Epoch 141
Validation auc = 0.744601
Epoch 142
Validation auc = 0.736150
Epoch 143
Validation auc = 0.727230
Epoch 144
Loss = 3.1218e-03, PNorm = 46.0609, GNorm = 1.9803, lr_0 = 7.9106e-04
Validation auc = 0.722066
Epoch 145
Validation auc = 0.715962
Epoch 146
Validation auc = 0.719718
Epoch 147
Validation auc = 0.732394
Epoch 148
Validation auc = 0.718310
Epoch 149
Loss = 2.1172e-03, PNorm = 46.1576, GNorm = 1.8403, lr_0 = 7.8430e-04
Validation auc = 0.715023
Epoch 150
Validation auc = 0.726291
Epoch 151
Validation auc = 0.736150
Epoch 152
Validation auc = 0.725352
Epoch 153
Validation auc = 0.706573
Epoch 154
Loss = 3.0594e-03, PNorm = 46.2406, GNorm = 1.5321, lr_0 = 7.7759e-04
Validation auc = 0.695775
Epoch 155
Validation auc = 0.693897
Epoch 156
Validation auc = 0.702817
Epoch 157
Validation auc = 0.713615
Epoch 158
Validation auc = 0.721127
Epoch 159
Loss = 1.4480e-03, PNorm = 46.3305, GNorm = 1.6895, lr_0 = 7.7095e-04
Validation auc = 0.726761
Epoch 160
Validation auc = 0.721127
Epoch 161
Validation auc = 0.708920
Epoch 162
Validation auc = 0.709390
Epoch 163
Validation auc = 0.714085
Epoch 164
Loss = 2.1396e-03, PNorm = 46.4268, GNorm = 1.4003, lr_0 = 7.6436e-04
Validation auc = 0.699061
Epoch 165
Validation auc = 0.699531
Epoch 166
Validation auc = 0.735211
Epoch 167
Validation auc = 0.740845
Epoch 168
Validation auc = 0.735211
Epoch 169
Loss = 3.0722e-03, PNorm = 46.5184, GNorm = 3.1193, lr_0 = 7.5782e-04
Validation auc = 0.733333
Epoch 170
Validation auc = 0.734272
Epoch 171
Validation auc = 0.730986
Epoch 172
Validation auc = 0.719249
Epoch 173
Validation auc = 0.712676
Epoch 174
Loss = 2.4497e-03, PNorm = 46.6210, GNorm = 1.6109, lr_0 = 7.5134e-04
Validation auc = 0.707042
Epoch 175
Validation auc = 0.706103
Epoch 176
Validation auc = 0.710329
Epoch 177
Validation auc = 0.714554
Epoch 178
Validation auc = 0.721596
Epoch 179
Loss = 2.3932e-03, PNorm = 46.6991, GNorm = 1.7228, lr_0 = 7.4492e-04
Validation auc = 0.724413
Epoch 180
Validation auc = 0.723944
Epoch 181
Validation auc = 0.723944
Epoch 182
Validation auc = 0.722535
Epoch 183
Validation auc = 0.713615
Epoch 184
Loss = 3.2045e-03, PNorm = 46.7782, GNorm = 2.4802, lr_0 = 7.3855e-04
Validation auc = 0.705634
Epoch 185
Validation auc = 0.701408
Epoch 186
Validation auc = 0.702817
Epoch 187
Validation auc = 0.705634
Epoch 188
Validation auc = 0.707042
Epoch 189
Loss = 1.4348e-03, PNorm = 46.8444, GNorm = 0.4586, lr_0 = 7.3224e-04
Validation auc = 0.706103
Epoch 190
Validation auc = 0.709859
Epoch 191
Validation auc = 0.728638
Epoch 192
Validation auc = 0.737089
Epoch 193
Validation auc = 0.736620
Epoch 194
Loss = 2.7681e-03, PNorm = 46.9366, GNorm = 1.9783, lr_0 = 7.2598e-04
Validation auc = 0.737089
Epoch 195
Validation auc = 0.729108
Epoch 196
Validation auc = 0.728169
Epoch 197
Validation auc = 0.730986
Epoch 198
Validation auc = 0.745540
Epoch 199
Loss = 1.6760e-03, PNorm = 47.0576, GNorm = 1.0481, lr_0 = 7.1977e-04
Validation auc = 0.747418
Epoch 200
Validation auc = 0.738967
Epoch 201
Validation auc = 0.737089
Epoch 202
Validation auc = 0.740376
Epoch 203
Validation auc = 0.740376
Epoch 204
Loss = 2.2511e-03, PNorm = 47.1368, GNorm = 0.7593, lr_0 = 7.1362e-04
Validation auc = 0.745540
Epoch 205
Validation auc = 0.743662
Epoch 206
Validation auc = 0.737089
Epoch 207
Validation auc = 0.732394
Epoch 208
Validation auc = 0.730516
Epoch 209
Loss = 9.4195e-04, PNorm = 47.1991, GNorm = 0.5011, lr_0 = 7.0752e-04
Validation auc = 0.725822
Epoch 210
Validation auc = 0.724883
Epoch 211
Validation auc = 0.721127
Epoch 212
Validation auc = 0.717371
Epoch 213
Validation auc = 0.715493
Epoch 214
Loss = 1.0538e-03, PNorm = 47.2593, GNorm = 1.1350, lr_0 = 7.0147e-04
Validation auc = 0.713146
Epoch 215
Validation auc = 0.718310
Epoch 216
Validation auc = 0.719718
Epoch 217
Validation auc = 0.717371
Epoch 218
Validation auc = 0.717371
Epoch 219
Loss = 1.3154e-03, PNorm = 47.3058, GNorm = 0.2412, lr_0 = 6.9548e-04
Validation auc = 0.726761
Epoch 220
Validation auc = 0.730516
Epoch 221
Validation auc = 0.730516
Epoch 222
Validation auc = 0.729577
Epoch 223
Validation auc = 0.728169
Epoch 224
Loss = 2.2101e-03, PNorm = 47.3520, GNorm = 0.3947, lr_0 = 6.8953e-04
Validation auc = 0.723944
Epoch 225
Validation auc = 0.724883
Epoch 226
Validation auc = 0.725352
Epoch 227
Validation auc = 0.723474
Epoch 228
Validation auc = 0.722066
Epoch 229
Loss = 6.0754e-04, PNorm = 47.3980, GNorm = 1.2061, lr_0 = 6.8364e-04
Validation auc = 0.723005
Epoch 230
Validation auc = 0.723474
Epoch 231
Validation auc = 0.730047
Epoch 232
Validation auc = 0.729108
Epoch 233
Validation auc = 0.723944
Epoch 234
Loss = 6.1238e-04, PNorm = 47.4476, GNorm = 1.1914, lr_0 = 6.7779e-04
Validation auc = 0.718779
Epoch 235
Validation auc = 0.720188
Epoch 236
Validation auc = 0.729108
Epoch 237
Validation auc = 0.735681
Epoch 238
Validation auc = 0.733803
Epoch 239
Loss = 1.4190e-03, PNorm = 47.5040, GNorm = 1.0178, lr_0 = 6.7200e-04
Validation auc = 0.733803
Epoch 240
Validation auc = 0.727230
Epoch 241
Validation auc = 0.724883
Epoch 242
Validation auc = 0.722066
Epoch 243
Validation auc = 0.715962
Epoch 244
Loss = 1.6854e-03, PNorm = 47.5656, GNorm = 2.3036, lr_0 = 6.6625e-04
Validation auc = 0.709859
Epoch 245
Validation auc = 0.708920
Epoch 246
Validation auc = 0.709859
Epoch 247
Validation auc = 0.706103
Epoch 248
Validation auc = 0.709859
Epoch 249
Loss = 7.6418e-04, PNorm = 47.6101, GNorm = 1.2542, lr_0 = 6.6056e-04
Validation auc = 0.707512
Epoch 250
Validation auc = 0.708451
Epoch 251
Validation auc = 0.707981
Epoch 252
Validation auc = 0.706103
Epoch 253
Validation auc = 0.708920
Epoch 254
Loss = 1.0651e-03, PNorm = 47.6506, GNorm = 0.6461, lr_0 = 6.5491e-04
Validation auc = 0.716901
Epoch 255
Validation auc = 0.724883
Epoch 256
Validation auc = 0.730516
Epoch 257
Validation auc = 0.731455
Epoch 258
Validation auc = 0.732394
Epoch 259
Loss = 7.4784e-04, PNorm = 47.6932, GNorm = 0.4000, lr_0 = 6.4931e-04
Validation auc = 0.730986
Epoch 260
Validation auc = 0.730516
Epoch 261
Validation auc = 0.729108
Epoch 262
Validation auc = 0.721127
Epoch 263
Validation auc = 0.722535
Epoch 264
Loss = 8.9806e-04, PNorm = 47.7363, GNorm = 1.4318, lr_0 = 6.4376e-04
Validation auc = 0.725352
Epoch 265
Validation auc = 0.728638
Epoch 266
Validation auc = 0.725822
Epoch 267
Validation auc = 0.726291
Epoch 268
Validation auc = 0.723005
Epoch 269
Loss = 5.6689e-04, PNorm = 47.7717, GNorm = 0.4265, lr_0 = 6.3826e-04
Validation auc = 0.722535
Epoch 270
Validation auc = 0.720657
Epoch 271
Validation auc = 0.716901
Epoch 272
Validation auc = 0.707981
Epoch 273
Validation auc = 0.703756
Epoch 274
Loss = 2.1117e-04, PNorm = 47.8182, GNorm = 0.1471, lr_0 = 6.3280e-04
Validation auc = 0.698592
Epoch 275
Validation auc = 0.702347
Epoch 276
Validation auc = 0.704225
Epoch 277
Validation auc = 0.704695
Epoch 278
Validation auc = 0.709390
Epoch 279
Loss = 8.7698e-04, PNorm = 47.8548, GNorm = 1.1561, lr_0 = 6.2739e-04
Validation auc = 0.711268
Epoch 280
Validation auc = 0.716901
Epoch 281
Validation auc = 0.722066
Epoch 282
Validation auc = 0.722535
Epoch 283
Validation auc = 0.718310
Epoch 284
Loss = 5.5026e-04, PNorm = 47.8968, GNorm = 0.9805, lr_0 = 6.2203e-04
Validation auc = 0.712207
Epoch 285
Validation auc = 0.702347
Epoch 286
Validation auc = 0.705634
Epoch 287
Validation auc = 0.715962
Epoch 288
Validation auc = 0.716901
Epoch 289
Loss = 9.3044e-04, PNorm = 47.9399, GNorm = 2.2766, lr_0 = 6.1671e-04
Validation auc = 0.720657
Epoch 290
Validation auc = 0.716901
Epoch 291
Validation auc = 0.719718
Epoch 292
Validation auc = 0.728638
Epoch 293
Validation auc = 0.732864
Epoch 294
Loss = 2.0017e-03, PNorm = 47.9859, GNorm = 1.9324, lr_0 = 6.1144e-04
Validation auc = 0.730986
Epoch 295
Validation auc = 0.729108
Epoch 296
Validation auc = 0.728638
Epoch 297
Validation auc = 0.730986
Epoch 298
Validation auc = 0.731925
Epoch 299
Loss = 6.2402e-04, PNorm = 48.0291, GNorm = 0.8277, lr_0 = 6.0621e-04
Validation auc = 0.733803
Model 0 best validation auc = 0.817840 on epoch 5
Loading pretrained parameter "encoder.encoder.cached_zero_vector".
Loading pretrained parameter "encoder.encoder.W_i.weight".
Loading pretrained parameter "encoder.encoder.W_h.weight".
Loading pretrained parameter "encoder.encoder.W_o.weight".
Loading pretrained parameter "encoder.encoder.W_o.bias".
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
Loading pretrained parameter "ffn.4.weight".
Loading pretrained parameter "ffn.4.bias".
Moving model to cuda
Model 0 test auc = 0.872366
Ensemble test auc = 0.872366
10-fold cross validation
Seed 0 ==> test auc = 0.912101
Seed 1 ==> test auc = 0.872968
Seed 2 ==> test auc = 0.895846
Seed 3 ==> test auc = 0.860927
Seed 4 ==> test auc = 0.911499
Seed 5 ==> test auc = 0.889825
Seed 6 ==> test auc = 0.934377
Seed 7 ==> test auc = 0.906683
Seed 8 ==> test auc = 0.937989
Seed 9 ==> test auc = 0.872366
Overall test auc = 0.899458 +/- 0.024672
